TSQ Endura and TSQ Quantiva Hardware Manual Revision B

TSQ Endura and TSQ Quantiva Hardware Manual Revision B
TSQ Series
TSQ Endura and
TSQ Quantiva
Hardware Manual
80100-97014 Revision B
August 2015
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product operation. This document is copyright protected and any reproduction of the whole or any part of this
document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of
Sale shall govern all conflicting information between the two documents.
Release history: Rev A, Sept. 2013; Rev B, August 2015
Software version: (Thermo) Foundation 3.0 and later, Xcalibur 2.3 and later, Tune 1.0 and later
For Research Use Only. Not for use in diagnostic procedures.
Regulatory Compliance
Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with
applicable domestic and international regulations. When the system is delivered to you, it meets all pertinent
electromagnetic compatibility (EMC) and safety standards as described in the next section or sections by product name.
Changes that you make to your system may void compliance with one or more of these EMC and safety standards.
Changes to your system include replacing a part or adding components, options, or peripherals not specifically
authorized and qualified by Thermo Fisher Scientific. To ensure continued compliance with EMC and safety standards,
replacement parts and additional components, options, and peripherals must be ordered from Thermo Fisher Scientific
or one of its authorized representatives.
EMC Directive 2004/108/EC
EMC compliance has been evaluated by TÜV Rheinland of North America.
EN 55011: 2009, A1: 2010
EN 61000-4-6: 2009
EN 61000-3-2: 2006, A2: 2009
EN 61000-4-11: 2004
EN 61000-3-3: 2008
EN 61326-1: 2013
EN 61000-4-2: 2009
CISPR 11: 2009, A1: 2010
EN 61000-4-3: 2006, A2: 2010
ICES-003 Issue 5: 2012
EN 61000-4-4: 2004, A1: 2010
CFR 47, FCC Part 15, Subpart B, Class A: 2012
EN 61000-4-5: 2006
Low Voltage Safety Compliance
This device complies with Low Voltage Directive 2006/95/EC and harmonized standard EN 61010-1:2010 (3rd
edition).
FCC Compliance Statement
THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES. OPERATION IS SUBJECT TO
THE FOLLOWING TWO CONDITIONS: (1) THIS DEVICE MAY NOT CAUSE HARMFUL
INTERFERENCE, AND (2) THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED,
INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION.
CAUTION Read and understand the various precautionary notes, signs, and symbols contained inside
this manual pertaining to the safe use and operation of this product before using the device.
Notice on Lifting and Handling of
Thermo Scientific Instruments
For your safety, and in compliance with international regulations, the physical handling of this Thermo Fisher Scientific
instrument requires a team effort to lift and/or move the instrument. This instrument is too heavy and/or bulky for one
person alone to handle safely.
Notice on the Proper Use of
Thermo Scientific Instruments
In compliance with international regulations: This instrument must be used in the manner specified by Thermo Fisher
Scientific to ensure protections provided by the instrument are not impaired. Deviations from specified instructions on
the proper use of the instrument include changes to the system and part replacement. Accordingly, order replacement
parts from Thermo Fisher Scientific or one of its authorized representatives.
WEEE Directive
2012/19/EU
Thermo Fisher Scientific is registered with B2B Compliance (B2Bcompliance.org.uk) in the UK and with the
European Recycling Platform (ERP-recycling.org) in all other countries of the European Union and in Norway.
If this product is located in Europe and you want to participate in the Thermo Fisher Scientific Business-to-Business
(B2B) Recycling Program, send an email request to [email protected] with the following information:
• WEEE product class
• Name of the manufacturer or distributor (where you purchased the product)
• Number of product pieces, and the estimated total weight and volume
• Pick-up address and contact person (include contact information)
• Appropriate pick-up time
• Declaration of decontamination, stating that all hazardous fluids or material have been removed from the product
For additional information about the Restriction on Hazardous Substances (RoHS) Directive for the European Union,
search for RoHS on the Thermo Fisher Scientific European language websites.
IMPORTANT This recycling program is not for biological hazard products or for products that have been medically
contaminated. You must treat these types of products as biohazard waste and dispose of them in accordance with
your local regulations.
Directive DEEE
2012/19/EU
Thermo Fisher Scientific s'est associé avec une ou plusieurs sociétés de recyclage dans chaque état membre de l’Union
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la page www.thermoscientific.fr/rohs.
WEEE Direktive
2012/19/EU
Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs-/Entsorgungsfirmen in allen EU-Mitgliedsstaaten
getroffen, damit dieses Produkt durch diese Firmen wiederverwertet oder entsorgt werden kann. Weitere Informationen
finden Sie unter www.thermoscientific.de/rohs.
C
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Cautions and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
Thermo Scientific
Chapter 1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Mass Spectrometer Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
TSQ Endura MS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
TSQ Quantiva MS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Overview of an LC/MS Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
LC/MS Functional Block Diagram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Electronic Assemblies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Controls and Indicators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
LEDs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Power Entry Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Communications Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Cooling Fans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Chapter 2
Scan Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Scan Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Full Scan Q1 and Q3 Scan Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Selected Ion Monitoring Scan Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Product Scan Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Precursor Scan Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Neutral Loss Scan Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Selected Reaction Monitoring Scan Type . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Scan Mass-To-Charge Ratio Ranges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Data Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Ion Polarity Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Chapter 3
Vacuum System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
Vacuum System Functional Block Diagram . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Schematic of the Internal Gas Supply Lines. . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
TSQ Endura and TSQ Quantiva Hardware Manual
vii
Contents
Inlet Gases Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Nitrogen Gas Valves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Argon Gas Valves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Vent Valve. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Vacuum Manifold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Vacuum Gauges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Vacuum Pumps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Atmospheric Pressure Ionization Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
API Source Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
viii
Chapter 4
Ion Transmission and Mass Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35
Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
MP00 Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
MP0 Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Mass Analyzers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Quadrupole Rod Assemblies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Applied RF and DC Fields . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Mass Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Collision Cell and CID Efficiency . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Quadrupole Offset Voltage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Mass Analyzer Lenses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Dual-Mode, Discrete-Dynode Ion Detection System . . . . . . . . . . . . . . . . . . . . 43
Chapter 5
Syringe Pump and Divert/Inject Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .45
Syringe Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Divert/Inject Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Configurations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Controlling the Divert/Inject Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Chapter 6
System Shutdown, Startup, and Reset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .49
Shutting Down the System in an Emergency. . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Placing the System in Standby Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Turning On the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Shutting Down the Mass Spectrometer Completely . . . . . . . . . . . . . . . . . . . . . 51
Starting the System after a Complete Shutdown . . . . . . . . . . . . . . . . . . . . . . . . 52
Starting the LC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Starting the Data System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Starting the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Starting the Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Resetting the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Resetting Calibration Parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Restarting the Data System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
On/Off Status for MS Components Under Varying Power Conditions. . . . . . . 56
TSQ Endura and TSQ Quantiva Hardware Manual
Thermo Scientific
Contents
Chapter 7
Daily Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .59
Before Operating the Mass Spectrometer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Checking the System Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Checking the Vacuum Pressure Levels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Checking the Gas Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
After Operating the Mass Spectrometer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Flushing the Inlet Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Purging the Oil in the Forepump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Emptying the Solvent Waste Container. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Placing the System in Standby Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Chapter 8
Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .65
Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Maintenance Schedule. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Tools and Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Maintaining the API Source Housing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Maintaining the API Source Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Cleaning the Ion Sweep Cone, Spray Cone, and Ion Transfer Tube . . . . . . . 70
Removing the API Source Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Cleaning the RF Lens, Exit Lens, MP00 RF Lens, and Lens L0. . . . . . . . . . . 76
Reinstalling the API Source Interface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Maintaining the Forepumps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Maintaining the Air Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Chapter 9
Diagnostics and PCB and Assembly Replacement. . . . . . . . . . . . . . . . . . . . . . . . .83
Running the System Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Replacing Fuses, PCBs, and Power Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Chapter 10
Replaceable Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .85
TSQ Chemical Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Calibration Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
MS Setup Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Performance Specification Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Single Mechanical Pump Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Dual Mechanical Pumps Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
TSQ Source Installation Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
API Source Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Miscellaneous Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .91
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .97
Thermo Scientific
TSQ Endura and TSQ Quantiva Hardware Manual
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Contents
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TSQ Endura and TSQ Quantiva Hardware Manual
Thermo Scientific
F
Figures
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Figure 34.
Figure 35.
Thermo Scientific
Functional block diagram of the TSQ Endura and TSQ Quantiva systems . . . . . 5
LEDs on the front panel of the mass spectrometer . . . . . . . . . . . . . . . . . . . . . . . . 6
Power entry module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Communication connectors (right side of the MS) . . . . . . . . . . . . . . . . . . . . . . . 9
Illustration of product scan type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Illustration of the precursor scan type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Illustration of the neutral loss scan type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Examples of compounds with a common neutral-loss fragment . . . . . . . . . . . . . 19
Functional block diagram of the vacuum system . . . . . . . . . . . . . . . . . . . . . . . . 24
Schematic of the internal gas supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Gas inlets and vacuum (foreline) port (left side of the mass spectrometer) . . . . . 25
Placement of the turbomolecular pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Ion Max NG and EASY-Max NG ion sources . . . . . . . . . . . . . . . . . . . . . . . . . . 30
API source interface (TSQ Endura MS cross section) . . . . . . . . . . . . . . . . . . . . 31
Ion transfer tubes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
RF and exit lenses for the mass spectrometers . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Schematic of the mass spectrometer ion transmission path . . . . . . . . . . . . . . . . . 35
MP00 rf lens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Lens L0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Multipole MP0 and beam blocker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
TK1 (left) and TK2 (right) lenses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Quadrupole Q1 or Q3 (TSQ Endura MS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Hyperquad Q1 or Q3 (TSQ Quantiva MS) . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Quadrupole Q2 (bottom) separated from the active collision cell housing
(top) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Polarity of the rf and dc voltages applied to the Q1 and Q3 mass analyzers . . . . 39
Magnitude of the asymmetric rf and dc voltages applied to the Q1 and Q3
rods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Syringe pump setup (top view) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Divert/inject valve positions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Divert/inject valve plumbed as a loop injector and as a divert valve . . . . . . . . . . 48
Divert/inject valve (front view) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
TSQ Endura Tune window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Ion sweep cone removed from the MS mount assembly . . . . . . . . . . . . . . . . . . 72
Ion transfer tube removal tool (TSQ Endura MS) . . . . . . . . . . . . . . . . . . . . . . . 72
Ion transfer removal tool (TSQ Quantiva MS) . . . . . . . . . . . . . . . . . . . . . . . . . 73
Spray cone, O-ring, ion transfer tube, and ion sweep cone (TSQ Endura MS) . . 73
TSQ Endura and TSQ Quantiva Hardware Manual
xi
Figures
Figure 36.
Figure 37.
Figure 38.
Figure 39.
Figure 40.
xii
API source interface removed from the vacuum manifold (TSQ Endura MS). .
Removing the multipole MP00 and lens L0 assembly . . . . . . . . . . . . . . . . . . . .
Removing the rf lens and exit lens (TSQ Endura MS) . . . . . . . . . . . . . . . . . . .
Removing the lens L0 and multipole MP00 from the MP00-L0 mount cage . .
Air filter location in the mass spectrometer with the front cover removed . . . . .
TSQ Endura and TSQ Quantiva Hardware Manual
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77
78
78
81
Thermo Scientific
P
Preface
This TSQ Endura and TSQ Quantiva Hardware Manual describes the modes of operation and
principle hardware components for the Thermo Scientific™ TSQ Endura™ and
TSQ Quantiva™ mass spectrometers (MSs). It also provides the instruments’ cleaning and
maintenance procedures.
Note The TSQ Endura MS requires one forepump. The TSQ Quantiva MS requires two
forepumps.
Contents
• Related Documentation
• Cautions and Special Notices
• Contacting Us
Related Documentation
The TSQ Endura and TSQ Quantiva mass spectrometers include complete documentation.
In addition to this guide, you can also access the following documents as PDF files from the
data system computer:
• TSQ Endura and TSQ Quantiva Preinstallation Requirements Guide
• TSQ Endura and TSQ Quantiva Getting Connected Guide
• TSQ Endura and TSQ Quantiva Getting Started Guide
• Ion Max NG and EASY-Max NG Ion Sources User Guide
• Safety and Regulatory Guide
The TSQ Endura and TSQ Quantiva also ship with a printed copy of the Safety and
Regulatory Guide. This guide contains important safety information about Thermo
Scientific liquid chromatography (LC) and mass spectrometry (MS) systems. Make sure
that all lab personnel have read and have access to this document.
Thermo Scientific
TSQ Endura and TSQ Quantiva Hardware Manual
xiii
Preface
 To view the product manuals
From the Microsoft™ Windows™ taskbar, do the following:
• For the Thermo Scientific mass spectrometer, choose Start > All Programs >
Thermo Instruments > model x.x, and then open the applicable PDF file.
• For an LC instrument controlled by a Thermo application, choose Start > All
Programs > Thermo Instruments > Manuals > LC Devices and so on.
The TSQ Endura and TSQ Quantiva application also provides Help.
 To view the Help
Do the following as applicable:
• To access the Tune application Help, click the Options icon,
Tune Help.
, and then choose
• To access the Xcalibur™ Method Editor Help, choose the appropriate option from the
Help menu.
 To download user documentation from the Thermo Scientific website
1. Go to www.thermoscientific.com.
2. In the Search box, type the product name and press Enter.
3. In the left pane, select Documents & Videos, and then under Refine By Category, click
Operations and Maintenance.
4. (Optional) Narrow the search results or modify the display as applicable:
• For all related user manuals and quick references, click Operator Manuals.
• For installation and preinstallation requirements guides, click Installation
Instructions.
• For documents translated into a specific language, use the Refine By Language
feature.
• Use the Sort By options or the Refine Your Search box (above the search results
display).
5. Download the document as follows:
a. Click the document title or click Download to open the file.
b. Save the file.
xiv
TSQ Endura and TSQ Quantiva Hardware Manual
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Preface
Cautions and Special Notices
Make sure that you follow the cautions and special notices presented in this guide. Cautions
and special notices appear in boxes; those concerning safety or possible damage also have
corresponding caution symbols.
This guide uses the following types of cautions and special notices.
CAUTION Highlights hazards to humans, property, or the environment. Each CAUTION
notice is accompanied by an appropriate CAUTION symbol.
IMPORTANT Highlights information necessary to prevent damage to software, loss of
data, or invalid test results; or might contain information that is critical for optimal
performance of the system.
Note Highlights information of general interest.
Tip Highlights helpful information that can make a task easier.
The TSQ Endura and TSQ Quantiva Hardware Manual contains the following
caution-specific symbols (Table 1).
Table 1. Caution-specific symbols and their meanings (Sheet 1 of 2)
Symbol
Meaning
Chemical hazard: Observe Good Laboratory Practices (GLP) when
handling chemicals. Only work with volatile chemicals under a fume
or exhaust hood. Wear gloves and other protective equipment, as
appropriate, when handling toxic, carcinogenic, mutagenic, corrosive,
or irritant chemicals. Use approved containers and proper procedures
to dispose of waste oil and when handling wetted parts of the
instrument.
Heavy object: Never lift or move the instrument by yourself; you can
suffer personal injury or damage the instrument
Hot surface: Before touching the API source assembly, allow heated
components to cool.
Pinch point: Keep hands away from the specified areas.
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Preface
Table 1. Caution-specific symbols and their meanings (Sheet 2 of 2)
Symbol
Meaning
Risk of electric shock: This instrument uses voltages that can cause
electric shock and/or personal injury. Before servicing the instrument,
shut it down and disconnect it from line power. While operating the
instrument, keep covers on.
Risk of eye injury: Eye injury can occur from splattered chemicals or
airborne particles. Wear safety glasses when handling chemicals or
servicing the instrument.
Sharp object: Avoid handling the tip of the syringe needle.
Read and understand the following cautions that are specific to the shutdown of the mass
spectrometry system or to the removal of parts for cleaning.
CAUTION If you must turn off the mass spectrometer in an emergency, turn off the
main power switch located on the right-side power panel. This switch turns off all
power to the mass spectrometer, including the forepump, without harming components
within the system. However, do not use this method as part of the standard shutdown
procedure. Instead, see “Shutting Down the Mass Spectrometer Completely” on page 51.
To turn off the LC, autosampler, and data system computer in an emergency, use their
respective on/off switch or button.
CAUTION To avoid an electrical shock, be sure to follow the instructions in“Shutting
Down the Mass Spectrometer Completely” on page 51.
CAUTION Do not turn the instrument on if you suspect that it has incurred any kind of
electrical damage. Instead, disconnect the power supply cord and contact Thermo Fisher
Scientific technical support for a product evaluation. Do not attempt to use the
instrument until it has been evaluated. (Electrical damage might have occurred if the
system shows visible signs of damage or has been transported under severe stress.)
CAUTION Do not disconnect the power supply cord from the mass spectrometer while
the other end is still plugged into the electrical outlet.
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CAUTION Do not place objects (for example, the syringe pump or other containers with
liquids) on top of the instrument, unless instructed to in the documentation. Leaking
liquids might contact the electronic components and cause an electrical short circuit.
CAUTION Hot surface. Allow heated components to cool to room temperature
(approximately 20 minutes) before servicing them.
CAUTION Place the mass spectrometer in Standby (or Off) mode before you open the
atmospheric pressure ionization (API) source. The presence of atmospheric oxygen in
the API source when the mass spectrometer is on could be unsafe. (The mass spectrometer
automatically turns off when you open the API source; however, it is best to take this
added precaution.)
CAUTION Follow the instrument maintenance instructions. To avoid personal injury or
damage to the instrument, do not perform any servicing other than that contained in the
TSQ Endura and TSQ Quantiva Hardware Manual or related manuals unless you are
authorized to do so.
CAUTION Use care when changing vacuum pump oil. Treat drained vacuum pump oil
and pump oil reservoirs with care. Hazardous compounds introduced into the system
might have dissolved in the pump oil. Always use approved containers and procedures for
disposing of waste oil. Whenever a pump has been operating on a system used for the
analysis of toxic, carcinogenic, mutagenic, or corrosive/irritant chemicals, you must
decontaminate the pump and certify it as free of contamination before a Thermo Fisher
Scientific field service engineer repairs or makes adjustments or before it is sent back to the
factory for service.
Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need. You
can use your smartphone to scan a QR code, which opens your email application or browser.
Contact us
Thermo Scientific
Customer Service and Sales
Technical Support
(U.S.) 1 (800) 532-4752
(U.S.) 1 (800) 532-4752
(U.S.) 1 (561) 688-8731
(U.S.) 1 (561) 688-8736
TSQ Endura and TSQ Quantiva Hardware Manual
xvii
Preface
Contact us
Customer Service and Sales
Technical Support
us.customer-support.analyze
@thermofisher.com
us.techsupport.analyze
@thermofisher.com
 To find global contact information or customize your request
1. Go to www.thermoscientific.com.
2. Click Contact Us, select the Using/Servicing a Product option, and then
type the product name.
3. Use the phone number, email address, or online form.
 To find product support, knowledge bases, and resources
Go to www.thermoscientific.com/support.
 To find product information
Go to www.thermoscientific.com/lc-ms.
Note To provide feedback for this document:
• Send an email message to Technical Publications ([email protected]).
• Complete a survey at www.surveymonkey.com/s/PQM6P62.
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TSQ Endura and TSQ Quantiva Hardware Manual
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1
Introduction
The TSQ Endura and TSQ Quantiva mass spectrometers are members of the Thermo
Scientific family of mass spectrometers. The TSQ Endura and TSQ Quantiva systems consist
of the mass spectrometer, a syringe pump, a divert/inject valve, and the Thermo Xcalibur data
system.
Note The Glossary defines some of the terms used in this manual.
Contents
• Mass Spectrometer Models
• Overview of an LC/MS Analysis
• LC/MS Functional Block Diagram
• Electronic Assemblies
• Controls and Indicators
• Cooling Fans
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TSQ Endura and TSQ Quantiva Hardware Manual
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Introduction
Mass Spectrometer Models
Mass Spectrometer Models
For descriptions of the various hardware components, see Chapter 3, “Vacuum System,”
Chapter 4, “Ion Transmission and Mass Analysis,” and Chapter 5, “Syringe Pump and
Divert/Inject Valve.”
TSQ Endura MS
The TSQ Endura mass spectrometer contains a triple-quadrupole mass analyzer and includes
an external syringe pump, an external divert/inject valve, and the Thermo Scientific
EASY-Max NG™ API source. The instrument requires one forepump.
TSQ Quantiva MS
The TSQ Quantiva mass spectrometer also contains a triple-quadrupole mass analyzer and
includes the external syringe pump and divert/inject valve. However, the TSQ Quantiva MS
uses the Thermo Scientific Ion Max NG™ API source and requires two forepumps.
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1 Introduction
Overview of an LC/MS Analysis
Overview of an LC/MS Analysis
In a typical LC/MS analysis, the liquid chromatograph (LC) portion of the system separates a
mixture into its chemical components. The LC pump produces a solvent stream (the mobile
phase) that passes through an LC column (containing the stationary phase) under high
pressure. An autosampler introduces a measured quantity of sample into this solvent stream.
As the solvent stream passes through the LC column, the sample separates into its chemical
components. The rate at which the components of the sample elute from the column depends
on their relative affinities to the mobile phase and the solid particles that make up the column
packing.
As the separated chemical components exit the LC column, they pass through a sample
transfer line and enter the mass spectrometer for ionization and analysis. As the mass
spectrometer analyzes the ionized components and determines each mass-to-charge ratio
(m/z) and relative intensity, it sends a data stream to the data system computer.
When the system setup includes a syringe pump and divert/inject valve, there are four
additional ways to introduce a sample into the mass spectrometer, as described in Table 2.
Table 2. Methods of sample introduction into the mass spectrometer
Method
Description
Direct infusion
Connect the syringe pump directly to the atmospheric
pressure ionization (API) source of the mass spectrometer.
High-flow infusion
Use a union Tee to combine the flow from the syringe pump
with the flow from an LC pump.
Manual loop injection
Connect a sample loop, a needle port fitting, and an LC
pump to the divert/inject valve. After you fill the sample loop
with sample, switch the position of the divert/inject valve,
which places the contents of the sample loop in the path of
the solvent flow produced by the LC pump.
Automated loop injection
Connect a sample loop, an LC pump, and the syringe pump
to the divert/inject valve. After you connect the plumbing,
specify the flow rate at which the syringe pump fills the
sample loop. After the loop is filled, the data system triggers
an injection.
The TSQ Endura and TSQ Quantiva MSs consist of an API source, ion optics, a triple-stage
mass analyzer, and an ion detection system. The ion optics, mass analyzer, ion detection
system, and part of the API source are enclosed in a vacuum manifold.
Ionization of the sample takes place in the API source. The ionization technique is the specific
process used to ionize the sample. The ion optics transmit the ions produced in the API
source into the mass analyzer to determine the mass-to-charge ratio (m/z) (of the ions
produced in the API source). The polarity of the electric potentials applied to the API source
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TSQ Endura and TSQ Quantiva Hardware Manual
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1
Introduction
Overview of an LC/MS Analysis
and ion optics determines whether positively charged ions or negatively charged ions are
transmitted to the mass analyzer. You can set up data acquisition methods for the mass
spectrometer to analyze positively or negatively charged ions or to switch between these
polarity modes during a single run.
The data system serves as the user interface to the mass spectrometer, autosampler, LC pump,
and syringe pump. Refer to the Xcalibur Help for more information about the TSQ Endura
MS or TSQ Quantiva MS data processing and instrument control application.
Each sequence of loading a mass analyzer with ions followed by mass analysis of the ions is
called a scan. The mass spectrometer uses several different iterations of the selected ion
monitoring (SIM) scan type to load, fragment, and detect ions. The ability to vary not only
the ionization and ion polarity modes, but the scan mode and scan type, provides greater
flexibility in the instrumentation for solving complex analytical problems.
For information about the heated-electrospray (H-ESI), atmospheric pressure chemical
ionization (APCI), and atmospheric pressure photoionization (APPI) techniques, refer to the
Ion Max NG and EASY-Max NG Ion Sources User Guide. For information about the
nanoelectrospray ionization (nanoESI or NSI) technique, refer to the manual that came with
your NSI source.
The mass spectrometer’s triple-stage mass analyzer performs either one stage or two stages of
mass analysis:
Analysis by direct infusion or flow injection provides no chromatographic separation of
components in the sample before they pass into the mass spectrometer. The data system then
processes and stores the data.
• The TSQ Endura or TSQ Quantiva system operates as a conventional mass spectrometer
with one stage of mass analysis. The ion source ionizes the sample, and mass analysis of
the ion products occurs in the first rod assembly. The second and third rod assemblies
transmit the resulting mass-selected ions to the ion detection system.1
–or–
• The TSQ Endura or TSQ Quantiva system operates as a tandem mass spectrometer with
two stages of mass analysis. The ion source ionizes the sample, and mass analysis of the
ion products occurs in the first rod assembly. In this case, however, mass-selected ions
exiting the first rod assembly collide with an inert gas in the second rod assembly and
fragment to produce a set of ions known as product ions. (A chamber called the collision
cell surrounds the second rod assembly. The collision cell can be pressurized with an inert
gas.) The product ions undergo further mass analysis in the third rod assembly to detect
selected ions. Two stages of mass analysis yield far greater chemical specificity than a
single stage can achieve because of the system’s ability to select and determine two discrete
but directly related sets of masses.
1
4
You can also use the instrument as a single-stage mass spectrometer by transmitting the ions through the first and
second rod assemblies followed by mass analysis in the third rod assembly.
TSQ Endura and TSQ Quantiva Hardware Manual
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1 Introduction
LC/MS Functional Block Diagram
You can use the first stage of mass analysis to elucidate the structures of pure organic
compounds and the structures of the components within mixtures. Furthermore, in a second
stage of mass analysis, the mass spectrometer can fragment and separate each ionic fragment
of a molecule formed in the ion source to build up an entire structure for the molecule, piece
by piece. Therefore, the mass spectrometer makes it possible to investigate all pathways for the
formation and fragmentation of each ion in the mass spectrum.
The two stages of mass analysis are ideal for very selective and sensitive analysis by reducing
chemical noise in the final mass spectrum.
Each sequence of single- or two-stage mass analysis of the ions is called a scan. The mass
spectrometer uses several different scan modes and scan types to filter, fragment, or transmit
ions in the mass analyzer, including the ionization and ion polarity modes. This ability to vary
the scan mode and scan type provides greater flexibility in the instrumentation for solving
complex analytical problems.
LC/MS Functional Block Diagram
Figure 1 shows a functional block diagram of the TSQ Endura and TSQ Quantiva systems. A
sample transfer line connects the LC inlet device to the mass spectrometer. The LC device is
usually installed on the left side of the mass spectrometer. A dedicated holder that sits on top
of the mass spectrometer contains the syringe pump and divert/inject valve.
In a typical analysis by LC/MS, a sample is injected onto an LC column. The sample then
separates into its various components. The components elute from the LC column and pass
into the mass spectrometer for analysis.
Figure 1.
Functional block diagram of the TSQ Endura and TSQ Quantiva systems
Inlet
Mass spectrometer
Data system
Autosampler
(optional)
Printer
LC pump
(optional)
Syringe pump
(optional)
Divert/inject valve
API
source
Ion
optics
Mass
analyzer
Ion
detection
system
Vacuum
system
Thermo Scientific
Instrument
control
electronic
assemblies
Computer
Monitor
TSQ Endura and TSQ Quantiva Hardware Manual
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Introduction
Electronic Assemblies
Electronic Assemblies
The electronic assemblies that control the operation of the mass spectrometer are distributed
among various printed circuit boards (PCBs) and other modules, in the embedded computer,
and on or around the vacuum manifold of the mass spectrometer. You cannot service the
electronic assemblies.
Note If you need assistance, contact your local Thermo Fisher Scientific field service
engineer.
Controls and Indicators
This section describes the following controls and indicators for the TSQ Endura and
TSQ Quantiva MSs:
• LEDs
• Power Entry Module
• Communications Panel
LEDs
Figure 2 shows the LEDs on the instrument’s front panel, and Table 3 lists their different
states and descriptions.
Figure 2.
LEDs on the front panel of the mass spectrometer
Table 3. LEDs for the TSQ Endura and TSQ Quantiva MSs (Sheet 1 of 2)
6
LED
State
Description
Power
Green
The mass spectrometer is receiving power.
(The electronics service switch is in the Operating
Mode position.)
Off
The mass spectrometer is not receiving power.
(The electronics service switch is in the Service
Mode position.)
TSQ Endura and TSQ Quantiva Hardware Manual
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1 Introduction
Controls and Indicators
Table 3. LEDs for the TSQ Endura and TSQ Quantiva MSs (Sheet 2 of 2)
LED
State
Description
Vacuum
Green
The vacuum is within the allowable operating
range.
Yellow
The system bakeout is in progress or the vacuum
is outside the allowable operating range.
Off
The mass spectrometer is either off or in the
process of starting up.
Green
The mass spectrometer and data system are
communicating.
Yellow
The mass spectrometer and data system are trying
to establish a communication link.
Off
The mass spectrometer is off.
Green
The mass spectrometer is on.
Yellow
The mass spectrometer is in standby mode.
Off
The mass spectrometer is off.
Flashing blue
The mass spectrometer is on and scanning.
Off
The mass spectrometer is not scanning.
Communication
System
Scan
Power Entry Module
The mass spectrometer receives line power at 230 Vac ±10%, 5 A, 50/60 Hz through the
right-side power entry module (Figure 3).
Figure 3.
Power entry module
Electronics service switch
SV65 Pump Enable connector
(forepump on/off control)
AC Output receptacle
(reserved for future use)
Power In receptacle
(230 Vac)
Main Power switch
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Introduction
Controls and Indicators
Main Power Switch
In the Off position, the Main Power (circuit breaker) switch removes all power to the mass
spectrometer, including the external forepump or forepumps. In the On position, the mass
spectrometer receives power. In the standard operational mode, the switch stays in the On
position.
CAUTION To shut off all power to the mass spectrometer in an emergency, place the main
power circuit breaker switch (labeled Main Power) in the Off (down) position. Do not use
the electronics service switch.
Electronics Service Switch
The electronics service switch is a circuit breaker. In the Service Mode (down) position, the
switch removes power to all components of the mass spectrometer except for the fans and
vacuum system. This setting allows you to service nonvacuum system components with the
vacuum system still operating (that is, the forepump or forepumps are still on). In the
Operating Mode (up) position, all components of the mass spectrometer have power.
SV65 Pump Enable Connector
The mass spectrometer turns the forepump or forepumps on and off by using the relay control
cable that connects to the SV65 Pump Enable connector.
Communications Panel
The communications panel, which is located on the right side of the mass spectrometer,
provides a system Reset button, a contact closure interface (Peripheral Control), an analog
input connector, USB ports for the external syringe pump and divert/inject valve, and a
Gigabit Ethernet connection port for the data system computer.
When you briefly press the Reset button, the embedded processing system and digital
circuitry reset and the system software reloads from the data system. For more information,
see “Resetting the Mass Spectrometer” on page 54.
Figure 4 shows the communication connectors, and Table 4 lists the pin-out descriptions for
these connectors.
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TSQ Endura and TSQ Quantiva Hardware Manual
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1 Introduction
Controls and Indicators
Figure 4.
Communication connectors (right side of the MS)
Ethernet port
USB ports
Analog Input
connector
Peripheral Control
connector
Reset button
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Introduction
Controls and Indicators
Table 4. Pin-out descriptions for the communication connectors (Sheet 1 of 2)
Pin
Name
Description
–
Reset
Resets the instrument to a power-up state.
Note Use this button only if the instrument does not
respond to the control program on the data system
computer or if you need to restart the instrument
without turning off the electronics service switch.
Peripheral Control
1
Ground
Earth ground
2
5V
Provides a 5 Vdc, 500 mA output (with pin 1).
4
Start In
Receives the start signal from the contact closure
connection of a connected external device.
To activate this signal, the external device must pull the
signal either low (below 0.75 Vdc) or high (above
2.4 Vdc), depending on the polarity, for at least
100 ms by using a relay, an open-collector driver, or a
similar device that connects between pins 4 and 1.
Note In the Instrument Configuration window, set
the contact closure signal to “High-to-low edge” or
“Low-to-high edge,” whichever matches the setting
for the connected external device.
5
Ready Out
Provides a relay-driven programmable output signal to
the connected external device. The relay opens when a
method starts and closes when the method finishes.
Output: Maximum 24 Vdc, 3 A
6
Injection Hold
Provides a relay-driven programmable output signal to
the connected external device, such as a fraction
collector.
Output: Maximum 24 Vdc, 3 A
8
10
RO/IH
TSQ Endura and TSQ Quantiva Hardware Manual
Common (return) connection for the Ready Out and
Injection Hold pins
Thermo Scientific
1
Introduction
Cooling Fans
Table 4. Pin-out descriptions for the communication connectors (Sheet 2 of 2)
Pin
Name
Description
Analog Input
The two analog channels connect to two separate 12-bit analog-to-digital converters (ADC)
for on-demand conversion of the input voltage. The conversion rate depends on the mass
spectrometer rate.
1
Chassis
Earth ground (for pins 3 and 4)
3, 4
2V Max:
+ (positive, pin 3) and
– (negative, pin 4)
Provides a connection for an external device, such as an
LC instrument.
5
Chassis
Earth ground (for pins 7 and 8)
7, 8
10V Max:
+ (positive, pin 7) and
– (negative, pin 8)
Provides a connection for an external device, such as an
LC instrument.
Input: 0–2 Vdc (voltage clamps at 5 Vdc)
Input: 0–10 Vdc (voltage clamps at 15 Vdc)
Other connectors
–
USB (2 ports)
Provides a connection for the syringe pump and
divert/inject valve.
–
Ethernet 1000 Base T
Provides a connection for the Ethernet switch.
Cooling Fans
To maintain the appropriate internal temperatures, the mass spectrometer contains several
fans, including those in the power supply subassemblies, provide internal cooling for the mass
spectrometer. Cooling air enters through the three main air intake fans on the right side of the
mass spectrometer. Exhaust air exits the instrument from the back ventilation slots.
The only user-serviceable part is the air filter in front of the air intake fans. For the
recommended maintenance schedule, see Chapter 8, “Maintenance.”
CAUTION To ensure safety and proper cooling, always operate the mass spectrometer with
its covers in place. This is also necessary to comply with product safety and
electromagnetic interference regulations.
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Introduction
Cooling Fans
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2
Scan Parameters
This chapter describes some of the scan parameter settings that you set in the TSQ Endura or
TSQ Quantiva Tune application.
Contents
• Scan Types
• Scan Mass-To-Charge Ratio Ranges
• Data Types
• Ion Polarity Modes
Scan Types
The TSQ Endura and TSQ Quantiva mass spectrometers operate in a variety of scan types.
The most common can be divided into two categories: single mass spectrometry (MS) scan
types and MS/MS scan types. The scan types in each category are as follows:
• MS scan types: full scan (Q1), full scan (Q3), selected ion monitoring (SIM) scan (Q1),
and SIM scan (Q3)
• MS/MS scan types: product ion scan, precursor ion scan, neutral loss scan, and selected
reaction monitoring (SRM) scan type
The available modes depend on the number and type of rod assemblies and the voltages
applied to the rod assemblies.
The mass analyzers have three rod assemblies.1 The first and third rod assemblies, Q1 and Q3,
are quadrupoles, and the second rod assembly, Q2, is a square-profile quadrupole.
Rod assemblies can operate in either of two capacities:
• As ion transmission devices
• As mass analyzers
1
Thermo Scientific
A rod assembly is a regular array of metal rods. See “Mass Analyzers” on page 38.
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Scan Parameters
Scan Types
If you apply only rf voltage, a rod assembly serves as an ion transmission device that passes all
ions within a large range of mass-to-charge ratios (m/z) (that is, virtually all ions that are
present).
When you apply both rf and dc voltages to a rod assembly, ions of different mass-to-charge
ratios separate. This separation allows the rod assembly to serve as a mass analyzer.
On the mass spectrometer, the quadrupole rod assemblies can operate with both rf and
dc voltages or with only rf voltage. That is, Q1 and Q3 can act as either mass analyzers or ion
transmission devices. The Q2 rod assembly operates exclusively with rf voltage. Therefore, Q2
is always an ion transmission device. For a summary of how the rod assemblies function in
several of the major scan types, see Table 5.
.
Table 5. Summary of scan types
Scan type
Quadrupole Q1
Full scan (Q1)
Scana
Q2 collision cell
Pass all
Full scan (Q3)
Pass all ions.
Pass all ions.
Scan
SIM scan (Q1)
Setc
Pass all ions.
Pass all ions.
SIM scan (Q3)
Pass all ions.
Pass all ions.
Set
ions.b
ionsd;
Quadrupole Q3
Pass all ions.
Product ion scan
Set
Fragment
then
pass all fragments.
Scan
Precursor ion scan
Scan
Fragment ions; then
pass all fragments.
Set
Neutral loss scan
Scan
Fragment ions; then
pass all fragments.
Scan
SRM scan
Set
Fragment ions; then
pass all fragments.
Set
a
Full scan or transmission of selected ions.
b
Pass ions or fragments within a wide range of mass-to-charge ratios.
c
Set to pass ions of a single mass-to-charge ratio or a set of mass-to-charge ratios.
d
Collisions with argon gas cause ions to fragment.
Full Scan Q1 and Q3 Scan Types
The full scan Q1 and Q3 scan types perform only one stage of mass analysis. The mass
spectrum obtained is equivalent to the mass spectrum obtained from an instrument with a
single mass analyzer. In the one stage of analysis, the ion source forms ions that enter the
analyzer assembly. One of the mass analyzers (Q1 or Q3) is scanned to obtain a complete mass
spectrum. The other rod assemblies (Q2 and Q3, or Q1 and Q2, respectively) act as ion
transmission devices. The full scan Q1 scan type uses Q1 as the mass analyzer; the full scan
Q3 scan type uses Q3 as the mass analyzer.
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Scan Parameters
Scan Types
Use full-scan type experiments to determine or confirm the mass-to-charge ratios (identity) of
unknown compounds or the mass-to-charge ratio of each component in a mixture of
unknown compounds. (Generally, you need a full mass spectrum to determine the
mass-to-charge ratio of an unknown compound.)
The full scan gives you more information about an analyte than does the selected ion
monitoring (SIM) scan type, but a full scan does not yield the sensitivity that the other two
scan types can achieve. This scan type requires less time monitoring the signal for each ion
than in SIM or SRM. Full scan provides greater information but lower sensitivity than the
other two scan types.
Before you perform a SIM or an SRM experiment, you must know what ions or reactions you
are looking for. Therefore, you might use a full scan for SIM to determine the identity of an
analyte and to obtain its mass spectrum, and a full scan for SRM to determine the mass
spectrum and product mass spectra for precursor ions of interest. Then, you might use SIM or
SRM to do routine quantitative analysis of the compound.
Selected Ion Monitoring Scan Type
Selected ion monitoring (SIM) monitors a particular ion or set of ions. You can use SIM
experiments to detect small quantities of a target compound in a complex mixture when you
know the mass-to-charge ratio of the target compound. Therefore, SIM is useful in trace
analysis and in the rapid screening of a large number of samples for a target compound.
Because SIM monitors only a few ions, it can provide lower detection limits and greater speed
than the full-scan modes. SIM achieves lower detection limits because more time is spent
monitoring significant ions that are known to occur in the mass spectrum of the target
analyte. SIM can achieve greater speed because it monitors only a few ions of interest; it does
not monitor regions of the spectrum that are empty or have no ions of interest.
SIM can improve the detection limit and decrease analysis time, but it can also reduce
specificity. Because SIM monitors only specific ions, any compound that fragments to
produce those ions will appear to be the target compound, which can result in a false positive.
Product Scan Type
Product scan type performs two stages of analysis. In the first stage, the ion source forms ions
that enter Q1, which is set to transmit ions of one mass-to-charge ratio. Ions selected by this
first stage of mass analysis are called precursor ions. (As a result, Q1 is referred to as the
precursor mass analyzer, and the mass-to-charge ratio of ions transmitted by the precursor
mass analyzer is referred to as the precursor set mass.) After Q1 selects the precursor ions, they
enter Q2, which is surrounded by the collision cell.
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Scan Parameters
Scan Types
Note For ease of documenting the first, second, and third rod assemblies as separate
pieces of hardware, this manual refers to them as Q1, Q2, and Q3, respectively. However,
when discussing each rod assembly's function in MS/MS scan types, this manual uses the
terms precursor mass analyzer, collision cell (ion transmission device surrounded by the
collision cell), and product mass analyzer, respectively.
In the second stage of analysis, ions in the collision cell can fragment further to produce
product ions. Two processes produce product ions: by unimolecular decomposition of
metastable ions or by interaction with argon collision gas present in the collision cell. This
latter step is known as collision-induced dissociation (CID). Ions formed in the collision cell
enter the product mass analyzer (Q3) for the second stage of mass analysis. The product mass
analyzer is scanned to obtain a mass spectrum that shows the product ions produced from the
fragmentation of the selected precursor ion.
A mass spectrum obtained in the product scan type (product mass spectrum) is the mass
spectrum of a selected precursor ion.
Figure 5 illustrates the product scan type.
Figure 5.
Illustration of product scan type
Q2
RF Only + Ar
Q1 Set
Q3 Scanning
Q3 m/z
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Scan Parameters
Scan Types
Precursor Scan Type
The precursor scan type also uses two stages of analysis. In the first stage, the ion source forms
ions that are introduced into the precursor mass analyzer, which is scanned to transmit
precursor ions sequentially into the collision cell.
In the second stage of analysis, in the collision cell, precursor ions can fragment to produce
product ions by unimolecular decomposition of metastable ions or by CID. The collision cell
forms ions that enter the product mass analyzer, which transmits a selected product ion. (The
product set mass is the mass-to-charge ratio of ions transmitted by the product mass analyzer.)
The resulting spectrum shows all the precursor ions that fragment to produce the selected
product ion. For a mass spectrum obtained in the precursor scan type (precursor mass
spectrum), note that data for the mass-to-charge ratio axis is obtained from Q1 (the precursor
ions), whereas data for the ion intensity axis is obtained from Q3 (from monitoring the
product ion).
Figure 6 illustrates the precursor scan type.
Figure 6.
Illustration of the precursor scan type
Q2
RF Only + Ar
Q1 Scanning
Q3 Set
Q1 m/z
You can use experiments that employ the precursor scan type (precursor experiments) in
structure and fragmentation studies as well as in survey analyses of mixtures. In general,
precursor experiments detect all compounds that decompose to a common fragment. You can
use the experiments for the rapid detection of a series of structural homologs (for example,
substituted aromatics, phthalates, steroids, or fatty acids) that have a common fragment ion
(for example, m/z 149 for the phthalates).
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Scan Parameters
Scan Types
Neutral Loss Scan Type
In the neutral loss scan type, the two mass analyzers (Q1 and Q3) link together so that they
are scanned at the same rate over mass ranges of the same width. However, the respective mass
ranges, are offset by a selected mass so that the product mass analyzer scans a selected number
of mass units lower than the precursor mass analyzer.
As a result, the neutral loss scan type provides two stages of mass analysis. In the first stage, the
precursor mass analyzer (Q1) separates ions that form in the ion source by their
mass-to-charge ratios. These ions enter the collision cell.
In the second stage of analysis, ions in the collision cell can fragment further by metastable ion
decomposition or by CID to produce product ions. The product mass analyzer then separates
these product ions by their mass-to-charge ratio. Figure 7 shows the neutral loss scan type.
Examples of compounds with a common neutral loss fragment appear in Figure 8.
To detect an ion, between the time the ion leaves Q1 and enters Q3, it must lose a neutral
moiety whose mass (the neutral loss mass) is equal to the difference in the mass ranges being
scanned by the two mass analyzers. Therefore, a neutral loss mass spectrum is a spectrum that
shows all the precursor ions that lose a neutral species of a selected mass.
You can also perform a neutral gain (or association) experiment in which the mass range
scanned by Q3 is offset by a selected mass above the mass range scanned by Q1.
For a neutral loss (or neutral gain) mass spectrum, as for a precursor mass spectrum, Q1 (the
precursor ion) provides data for the mass-to-charge ratio axis, whereas Q3 (the product ion
being monitored) provides data for the ion intensity axis.
You can use experiments that use the neutral loss scan type (neutral loss experiments) when
surveying a large number of compounds for common functionality. However, you frequently
lose neutral moieties from substituent functional groups (for example, CO2 from carboxylic
acids, CO from aldehydes, HX from halides, and H2O from alcohols).
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Figure 7.
Scan Parameters
Scan Types
Illustration of the neutral loss scan type
Q2
RF Only + Ar
Q1 Scanning
Q3 = Q1 - 
Q1 m/z
Figure 8.
Examples of compounds with a common neutral-loss fragment
NH2
N
N
H2 N
N
HO
N
N
N
N
H2 N
N
N
H2 N
N
N
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Scan Parameters
Scan Mass-To-Charge Ratio Ranges
Selected Reaction Monitoring Scan Type
Selected reaction monitoring (SRM) monitors a particular transition or set of transitions, such
as the fragmentation of an ion or the loss of a neutral moiety.
SRM monitors a limited number of precursor or product ion pairs. In product-like
experiments, the mass spectrometer selects a precursor ion as usual, but generally it only
monitors one product ion. SRM experiments are normally conducted with the product scan
mode.
As does SIM, SRM provides for the very rapid analysis of trace components in complex
mixtures. However, because SRM selects two sets of ions, it obtains specificity that is much
greater than what SIM can obtain. Any interfering compound would have to form an ion
source product (precursor ion) of the same mass-to-charge ratio as the selected precursor ion
from the target compound. Furthermore, that precursor ion would have to fragment to form a
product ion of the same mass-to-charge ratio as the selected product ion from the target
compound.
Scan Mass-To-Charge Ratio Ranges
The TSQ Endura MS can operate in a mass-to-charge ratio range of m/z 10–3400. The
TSQ Quantiva MS can operate in a mass-to-charge ratio range of m/z 10–1800.
Data Types
With the TSQ Endura or TSQ Quantiva MS, you can acquire and display mass spectral data
(intensity versus mass-to-charge ratio) in one of two data types:
• Profile data
With profile data, you can see the inherent shape of the peaks in the mass spectrum. The
mass spectrum divides each atomic mass unit into several sampling intervals. The
intensity of the ion current is determined at each sampling interval. The intensity at each
sampling interval is displayed with the intensities connected by a continuous line.
• Centroid data
With centroid data, you can see the mass spectrum as a bar graph. This scan data type
sums the intensities of each set of sampling intervals. This sum is displayed versus the
integral center of mass of the many sampling intervals. Centroid data requires about
one-tenth the computer disk space of what is required for profile data.
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Scan Parameters
Ion Polarity Modes
Ion Polarity Modes
The TSQ Endura and TSQ Quantiva MSs can operate in either positive or negative ion
polarity mode. The mass spectrometer controls whether positive ions or negative ions are
transmitted to the mass analyzer for mass analysis by changing the polarity of the voltage
potentials applied to the API source, ion optics, and ion detection system.
The information obtained from a positive ion mass spectrum is different from and
complementary to the information from a negative ion spectrum. Therefore, the ability to
obtain both positive ion and negative ion mass spectra aids you in the qualitative analysis of
your sample. You can choose the ion polarity mode and ionization mode to obtain maximum
sensitivity for the particular analyte of interest.
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Scan Parameters
Ion Polarity Modes
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Vacuum System
This chapter describes the principal components of the vacuum system for the TSQ Endura
and TSQ Quantiva mass spectrometers.
Contents
• Vacuum System Functional Block Diagram
• Schematic of the Internal Gas Supply Lines
• Inlet Gases Hardware
• Vacuum Manifold
• Vacuum Gauges
• Vacuum Pumps
• Atmospheric Pressure Ionization Source
• API Source Interface
Vacuum System Functional Block Diagram
The vacuum system evacuates the region around the API source interface, ion optics, mass
analyzer, and ion detection system. Figure 9 shows a functional block diagram of the vacuum
system with hyperlinks to the applicable sections.
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Vacuum System
Schematic of the Internal Gas Supply Lines
Figure 9.
Functional block diagram of the vacuum system
Nitrogen
gas port
Filtered air
Sheath
gas valve
Sweep
gas valve
Vent
valve
Aux gas
valve
Atmospheric
pressure
region
Sample input
device
Ion transfer
tube and rf
lens region
MP00
ion optics
region
Mass
analyzer
region
MP0
ion optics
region
Collision
cell
Ion
gauge
Sample tube
Triple-inlet
turbomolecular pump
Convection
vacuum gauge
Convection
vacuum gauge
Collision gas
divert valve
Exhaust
Forepump(s)
Foreline
Collision
gas valve
Argon
gas port
Schematic of the Internal Gas Supply Lines
Figure 10 shows a schematic drawing of the gas lines in the mass spectrometer.
Figure 10. Schematic of the internal gas supplies
API
source
Collision
cell
Source PCB
Gas box
(Left side of the MS)
UHP argon gas inlet
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HP nitrogen gas inlet
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3 Vacuum System
Inlet Gases Hardware
Inlet Gases Hardware
The inlet gases hardware controls the flow of the following gases into the mass spectrometer:
argon collision gas; nitrogen sheath gas, auxiliary gas, and sweep gas; and nitrogen venting gas.
Figure 11 shows the gas inlets on the left side of the mass spectrometer.
• Nitrogen Gas Valves
• Argon Gas Valves
• Vent Valve
Figure 11. Gas inlets and vacuum (foreline) port (left side of the mass spectrometer)
Argon gas inlet
Nitrogen gas inlet
Drain/waste
port
Vacuum (foreline)
port
Note For a list of guidelines for the operating parameters, refer to section “LC Flow Rate
Ranges” in Chapter 1 of the TSQ Endura and TSQ Quantiva Getting Started Guide.
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Vacuum System
Inlet Gases Hardware
Nitrogen Gas Valves
The data system controls the valves that regulate the nitrogen pressure (see “Checking the Gas
Supplies” on page 62). You can set the gas flow rates in the Ion Source pane of the Tune
application.
Dry nitrogen gas (690 ±140 kPa [100 ±20 psi], 99% purity) enters the left side of the mass
spectrometer through a 1/4 in. port. The valves for the sheath, auxiliary, and sweep gases
control the flow of dry nitrogen gas into the API source (Figure 9). Sheath gas is the
inner-coaxial nitrogen gas that helps nebulize the sample solution into a fine mist as the
solution exits the API spray insert nozzle. Auxiliary gas is the outer-coaxial nitrogen gas that
helps the sheath gas in the nebulization and evaporation of the sample solution by focusing
the vapor plume and lowering the humidity in the API source. Sweep gas is the off-axis
nitrogen gas that flows out from behind the optional ion sweep cone to aid in solvent
declustering and adduct reduction. The optional ion sweep cone has an inlet for the sweep
gas.
Argon Gas Valves
The data system controls the valves that regulate the argon gas pressure (see “Checking the
Gas Supplies” on page 62). You can set the collision gas pressure (CID gas) in the Tune
application.
Argon gas (135 ±70 kPa [20 ±10 psi], 99.995% minimum purity) enters the left side of the
mass spectrometer through a 1/8 in. port. The valves for the collision gas control the flow of
argon gas into and out of the Q2 collision cell. When activated, a solenoid valve shuts off the
argon gas flow to the cell.
Vent Valve
The solenoid-operated vent valve allows the vacuum manifold to be vented with filtered air.
The vent valve on the vacuum manifold is closed when the solenoid is energized.
The vacuum manifold vents when the mass spectrometer no longer receives external power, as
with a power failure or when you turn off the main power switch. Power is briefly provided to
the vent valve after losing external power to protect against the accidental loss of power. When
power to the vent valve solenoid shuts off for more than a very brief period of time, the vent
valve opens and the manifold vents air.
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Vacuum System
Vacuum Manifold
Vacuum Manifold
The vacuum manifold (Figure 12) is a thick-walled, aluminum chamber with multiple
removable top cover plates, various electrical feedthroughs, and gas inlets. It encloses the API
source interface, ion optics, mass analyzer, and ion detection system assemblies.
Table 6 lists the five vacuum regions, the pumps that evacuate them, and the chamber
pressures for both instruments. The block diagram in Figure 9 shows the vacuum regions.
Table 6. Vacuum regions, evacuation devices, and typical pressures
Region
Components
Evacuated by
Pressure
TSQ Endura
TSQ Quantiva
1
API source
N/A
Atmosphere
2
RF lens
Forepump or forepumps
3
MP00 ion optics
Triple-inlet turbomolecular pump
(first inlet [molecular drag])
50 mTorr
4
MP0 ion optics
Triple-inlet turbomolecular pump
(second inlet [interstage])
1 mTorr
5
Mass analyzer
Triple-inlet turbomolecular pump
(third inlet [high vacuum])
Less than10–5 Torr
Less than 2 Torr
Less than 4.5 Torr
Vacuum Gauges
The mass spectrometer contains three types of vacuum gauges that measure the pressure in
specific regions of the vacuum manifold. In the Tune application, you can observe the
readback values for the vacuum gauges on the By Function page in the Status pane (under
Vacuum).
• Convection pressure gauge—Measures pressure down to a fraction of a milliTorr (mT).
The instrument uses two convection gauges:
–
Source pressure gauge—Measures the pressure in the rf lens and API ion transfer tube
region in the vacuum manifold and the foreline, which connects the triple-inlet
turbomolecular pump and the forepump or forepumps.
–
Collision gas pressure gauge—Measures the pressure in the collision cell.
• Ion gauge—Measures the pressure in the analyzer region of the vacuum manifold.
The ion gauge produces energetic electrons that cause the ionization of molecules in the
ion gauge. A collector attracts positive ions formed in the ion gauge. The collector current
is related to the pressure in the vacuum manifold. The ion gauge is also involved in
vacuum protection.
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Vacuum System
Vacuum Pumps
Vacuum Pumps
The mass spectrometer requires either one (TSQ Endura MS) or two (TSQ Quantiva MS)
external forepumps, and both instruments require an internal turbomolecular pump to
provide the vacuum pressures for the five vacuum regions (Figure 9). The forepumps create
the vacuum necessary for the proper operation of the turbomolecular pump. It also evacuates
the ion transfer tube region of the vacuum manifold.
Each forepump’s detachable power supply cord connects to separate single-phase 230 Vac wall
outlets. However, the mass spectrometer can remotely turn the forepumps on and off through
the relay control cable that connects to the mass spectrometer’s SV65 Pump Enable connector
(Figure 3).
The instrument’s Main Power switch, not the electronics service switch, controls the SV65
Pump Enable connector and turns off the turbomolecular pump. If the temperature of the
turbomolecular pump becomes too high, however, power to the turbomolecular pump
automatically shuts off.
As shown in Figure 12, one triple-inlet turbomolecular pump controls the vacuum for
multiple vacuum regions. The turbomolecular pump also sends status information, such as its
temperature or rotational speed, to the data system computer.
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Vacuum System
Vacuum Pumps
Figure 12. Placement of the turbomolecular pump
Collision cell
chamber
Mass analyzer
chambers
MP0 ion optics
chamber
Turbomolecular
pump
MP00 ion optics
chamber
RF lens and ion transfer
tube chamber
Front
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Vacuum System
Atmospheric Pressure Ionization Source
Atmospheric Pressure Ionization Source
The atmospheric pressure ionization (API) source forms gas phase sample ions from sample
molecules that are contained in solution. The API source also serves as the interface between
the LC and the mass spectrometer. You can configure the EASY-Max NG API source
(provided with the TSQ Endura MS) or Ion Max NG API source (provided with the
TSQ Quantiva MS) for the following ionization techniques: H-ESI, APCI, and APPI.
The mass spectrometer has a front, built-in drain that routes the solvent waste from the API
source to the solvent waste container connected to the left-side drain/waste port. For
information about the solvent waste connection, refer to the TSQ Endura and TSQ Quantiva
Getting Connected Guide.
For information about the API source, refer to Chapter 2 in the TSQ Endura and
TSQ Quantiva Getting Started Guide. For instructions on how to install the spray insert, refer
to the Ion Max NG and EASY-Max NG Ion Sources User Guide.
Figure 13. Ion Max NG and EASY-Max NG ion sources
Spray insert depth adjustment
(Ion Max NG only)
Retainer knobs for spray insert and
heater assembly
Locking levers (locked position)
Grounding union holder
Rotational adjustment knobs
Window
Ion Max NG
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Vacuum System
API Source Interface
API Source Interface
The API source interface consists of the components of the API source that are held under
vacuum (except for the atmospheric pressure side of the ion sweep cone) in a vacuum chamber
that the forepump evacuates to a pressure of approximately 1.5 Torr (for the TSQ Endura
MS) or 4.0 Torr (for the TSQ Quantiva MS). The API source interface includes an ion sweep
cone, an ion transfer tube, two cartridge heaters, a heater block, a sensor, a vent prevent ball,
the rf lens, the exit lens, and lens L0 (Figure 14).
Figure 14. API source interface (TSQ Endura MS cross section)
Exit lens
Sweep gas cone
Vent prevent ball
RF lens
L0 lens
Ion transfer tube
Front
Spray cone
Heater block
MP00 multipole
The ion sweep cone is a metal cone over the ion transfer tube. The ion sweep cone channels
the sweep gas toward the entrance of the ion transfer tube, acts as a physical barrier that
protects the entrance of the ion transfer tube, and increases source robustness. The net result
is a significant increase in the number of samples to analyze without a loss of signal intensity.
In addition, keeping the ion transfer tube entrance as clean as possible reduces the need for
frequent maintenance. Install the ion sweep cone to improve ruggedness when analyzing
complex matrices such as plasma or nonvolatile salt buffers. Remove the ion sweep cone
before performing NSI experiments.
The ion transfer tube (Figure 15) is a metal, cylindrical tube that assists in desolvating ions
produced by the API spray insert while transferring them into the vacuum system. The regular
ion transfer tube has a 0.58 mm (0.02 in.) diameter orifice (TSQ Endura MS) and the
high-capacity ion transfer tube has a vertical 2 × 0.6 mm (0.08 × 0.02 in.) rectangular orifice
(TSQ Quantiva MS).
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Vacuum System
API Source Interface
Figure 15. Ion transfer tubes
TSQ Endura ion transfer tube
Front
TSQ Quantiva high-capacity
ion transfer tube (vertical orifice)
The heater block contains two heater cartridges, surrounds the ion transfer tube, and heats the
tube to temperatures up to 400 °C (752 °F). A thermocouple measures the temperature of the
heater block. Typical temperatures of the ion transfer tube are 270 °C (518 °F) for H-ESI and
250 °C (482 °F) for APCI, but these temperatures vary with the flow rate and the mobile
phase composition. A decreasing pressure gradient draws ions into the ion transfer tube in the
atmospheric pressure region and transports them to the API source interface region of the
vacuum manifold. The mass spectrometer applies the same electrical potential (positive for
positive ions and negative for negative ions) to the ion transfer tube and the rf lens, which
assists in transporting the ions from the tube to the rf lens. When you remove the ion transfer
tube (after it has cooled to room temperature), the vent prevent ball drops into place to stop
air from entering the vacuum manifold. Therefore, you can remove the ion transfer tube for
cleaning or replacement without venting the system.
Ions from the ion transfer tube pass through the rf lens and then the exit lens (Figure 16). The
rf lens is an ion transmission device consisting of progressively spaced, stainless-steel
electrodes. The rf lens differs slightly between the TSQ Endura MS and the TSQ Quantiva
MS. The mass spectrometer applies an rf voltage to the electrodes, and adjacent electrodes
have voltages of opposite phase. As the rf amplitude increases, ions of progressively higher
mass-to-charge ratios pass through to the exit lens and move toward the MP00 rf lens. The
exit lens acts as a vacuum baffle between the higher pressure API source interface region and
the lower pressure MP00 rf lens region of the vacuum manifold. The rf lens and exit lens
mount to the API source interface cage.
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Vacuum System
API Source Interface
Figure 16. RF and exit lenses for the mass spectrometers
TSQ Endura MS rf lens
Exit lens
TSQ Quantiva MS rf lens
Back
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Vacuum System
API Source Interface
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4
Ion Transmission and Mass Analysis
This chapter provides descriptions of the ion optics elements, mass analyzer, and ion detection
system in the TSQ Endura and TSQ Quantiva MSs.
Contents
• Ion Optics
• Mass Analyzers
• Dual-Mode, Discrete-Dynode Ion Detection System
Ion Optics
Figure 17 shows a schematic of the ion transmission path through the TSQ Endura and
TSQ Quantiva MSs with hyperlinks to the applicable sections.
Figure 17. Schematic of the mass spectrometer ion transmission path
Dual-mode, discrete-dynode detector
(inside)
Lenses EL31, EL32, EL33
Hyperquad Q3
mass analyzer
Lenses EL21, EL22, EL23
Hyperquad Q1
mass analyzer
Quadrupole Q2
mass analyzer
Multipole M0
MP00 rf lens and lens L0
RF lens and exit lens
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Ion Transmission and Mass Analysis
Ion Optics
The ion optics focus the gas-phase sample ions into the mass analyzer. This section describes
the following:
• MP00 Ion Optics
• MP0 Ion Optics
MP00 Ion Optics
Ions pass through the exit lens and move toward the MP00 ion optics, which are located
between the API source interface and the MP0 ion optics. The MP00 ion optics include the
MP00 rf lens and the L0 lens. For the location of these components, see Figure 17.
The MP00 rf lens is an array of eight metal elements (Figure 18). The mass spectrometer
applies an rf voltage to the elements, generating an electric field that guides the ions along the
axis of the lens.
A dc voltage offset from ground and applied to MP00 (called the MP00 offset voltage)
increases the translational kinetic energy (TKE) of ions emerging from the exit lens. During
ion focusing, the offset voltage is negative for positive ions and positive for negative ions.
Increasing the offset voltage increases the TKE of the ions.
Figure 18. MP00 rf lens
The lens L0 is a metal disk with a small hole in the center through which the ion beam passes
(Figure 19). The mass spectrometer applies an electrical potential (positive for positive ions
and negative for negative ions) to lens L0 to aid in ion transmission. Lens L0, which mounts
to the MP00 rf lens, also acts as a vacuum baffle between the MP00 and MP0 ion optics
chambers.
Figure 19. Lens L0
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Ion Optics
MP0 Ion Optics
The MP0 ion optics transmit ions from the MP00 ion optics to the mass analyzer. The MP0
ion optics include multipole MP0 and lenses TK1 and TK2. See Figure 17 for the location of
these components.
Multipole MP0 is an array of square-metal rods that act as an ion transmission device
(Figure 20). The mass spectrometer applies an rf voltage to the elements, generating an
electric field that guides the ions along the axis of the multipole. The MP0 offset voltage
increases the TKE of ions emerging from MP00. The rods are curved so that neutrally
charged species hit a beam blocker. This removes them from the beam.
Figure 20. Multipole MP0 and beam blocker
Beam blocker
The TK1 and TK2 lenses are metal discs with a circular hole in the center through which the
ion beam passes (Figure 21). Together they act as a two-element cone lens. The mass
spectrometer applies an electrical potential to the lens to accelerate (or decelerate) ions as they
approach each lens and to focus the ion beam as it passes through each lens. Lenses TK1 and
TK2 as a vacuum baffle between the multipole MP0 and quadrupole Q1.
Figure 21. TK1 (left) and TK2 (right) lenses
Front
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Ion Transmission and Mass Analysis
Mass Analyzers
Mass Analyzers
This section describes the components of the mass analyzer, voltages applied to the mass
analyzer electrodes, and mass analyzer operation during mass analysis. Ion manipulation and
mass analysis occur in a mass analyzer, which consists of three quadrupole rod assemblies (Q1,
Q2, and Q3) and two lens sets (EL21, EL22, EL23 and EL31, EL32, EL33). See Figure 17.
The following subtopics discuss the mass analyzer in detail:
• Quadrupole Rod Assemblies
• Applied RF and DC Fields
• Mass Analysis
• Collision Cell and CID Efficiency
• Quadrupole Offset Voltage
• Mass Analyzer Lenses
Quadrupole Rod Assemblies
The three rod assemblies in the mass analyzers are numbered from the API source end of the
manifold and are designated Q1, Q2, and Q3 (Figure 17). Quadrupoles Q1 and Q3 enable
high-resolution scans without signal loss.
For the TSQ Endura MS, quadrupoles Q1 and Q3 (also known as a hyperquads) are square
arrays of circular rods (Figure 22). For the TSQ Quantiva MS, quadrupoles Q1 and Q3 are
square arrays of precision-machined and precision-aligned, true hyperbolic rods (Figure 23).
Quartz spacers act as electrical insulators between adjacent rods.
Figure 22. Quadrupole Q1 or Q3 (TSQ Endura MS)
Figure 23. Hyperquad Q1 or Q3 (TSQ Quantiva MS)
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Mass Analyzers
Quadrupole Q2 is a square-profile quadrupole rod assembly that always acts as an ion
transmission device. The rods bend into a 90-degree arc (Figure 24), which in addition to
reducing the footprint of the instrument, prevent the transmission of unwanted neutral
species to the detector and dramatically lower the noise level in the data.
Quadrupole Q2 has become synonymous with the term active collision cell. Technically, the
collision cell is the chamber that encloses Q2 where CID can take place if the argon or
nitrogen collision gas is present. The active collision cell has an axial field down its length to
speed throughput. This allows up to 500 SRM transitions per second.
Figure 24. Quadrupole Q2 (bottom) separated from the active collision cell housing (top)
EL21, EL22, and
EL23 lenses
EL31, EL32, and
EL33 lenses
Applied RF and DC Fields
In a quadrupole rod assembly, because rods opposite each other in the array connect
electrically, the four rods are considered two pairs of two rods each. The mass spectrometer
applies rf and dc voltages to the rods. As shown in Figure 25, although the rf voltages applied
to the four rods are the same, the two pairs are 180 degrees out of phase (that is, one pair has
a positive voltage and the other a negative voltage).
Figure 25. Polarity of the rf and dc voltages applied to the Q1 and Q3 mass analyzers
RF voltage + dc voltage
RF voltage 180° out of phase – dc voltage
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Ion Transmission and Mass Analysis
Mass Analyzers
The quadrupole coil module provides the voltages for operating the quadrupole. The rf
voltage applied to the quadrupole rods is of constant frequency (approximately 1.095 MHz
for the TSQ Endura MS and 1.005 MHz for the TSQ Quantiva MS). The rf voltage applied
to one rod pair has 90% of the amplitude and is opposite in sign of the other rod pair. This is
referred to as asymmetric rf, which increases ion transmission by decreasing the fringe fields at
the ends of the rods. See Figure 26.
Because the frequency of this ac voltage is in the radio frequency range, it is referred to as rf
voltage. In Figure 26, the solid line represents the combined rf and dc voltage applied to one
rod pair, and the dashed line represents the combined rf and dc voltage applied to the other
rod pair. The ratio of rf voltage to dc voltage determines the ability of the mass spectrometer
to separate ions of different mass-to-charge ratios.
As mentioned, the first and third quadrupole rod assemblies (Q1 and Q3) can act as mass
analyzers or as ion transmission devices. When the mass spectrometer applies both rf and dc
voltages, quadrupoles Q1 and Q3 act as mass analyzers, and when it applies only rf voltage,
they act as ion transmission devices. In the ion transmission mode, the quadrupoles allow ions
in a wide window of mass-to-charge ratios to pass.
The square quadrupole rod assembly (Q2) operates in the ion transmission mode only.
Surrounding quadrupole Q2 is a collision cell where CID takes place if the argon or nitrogen
collision gas is present in the cell.
Figure 26. Magnitude of the asymmetric rf and dc voltages applied to the Q1 and Q3 rods
RF voltage
10 0000 V p/p
900 Vdc
Voltage
(v)
RF voltage
90000 V p/p
–900 Vdc
Atomic mass units
(u)
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Mass Analyzers
Mass Analysis
The mass analyzers (quadrupoles Q1 and Q3) are square arrays that are charged with a
variable ratio of rf voltage and dc voltage (Figure 26). These potentials give rise to an
electrostatic field that gives stable oscillations to ions with a specific mass-to-charge ratio and
unstable oscillations to all others.
At any given instant, the mass analyzer applies one particular set of rf and dc voltage values to
the mass analyzer rods. Under these conditions, only ions of one mass-to-charge ratio (for
example, m/z 180) are maintained within bounded oscillations as their velocity carries them
through the mass analyzer. At the same time, all other ions undergo unbounded oscillations.
These ions strike one of the rod surfaces, become neutralized, and are pumped away, or they
are ejected from the rod assembly.
Then, at a later time, both rf and dc voltages change, and ions of the next mass-to-charge ratio
(for example, m/z 181) are allowed to pass, while all other ions (including m/z 180) become
unstable and undergo unbounded oscillations. This process of transmitting ions of one
mass-to-charge ratio after another continues as the rf and dc voltages change in value. At the
end of the scan, the rf and dc voltages are discharged to zero, and the process repeats.
The mass spectrometer can rapidly and precisely change the potentials on the quadrupole rods
to obtain a fast scan rate.
The more closely the electrostatic field generated by a set of quadrupole rods approximates a
hyperbolic geometry, the better their operating characteristics are. As a result, the mass
spectrometer’s precision quadrupole rods provide excellent sensitivity, peak shape, resolution,
and high mass transmission.
Collision Cell and CID Efficiency
In the MS/MS scan modes, the mass spectrometer applies a large voltage of opposite polarity
to the rod pairs between scans, which empties the collision cell. This process ensures that no
ions remain in the collision cell from scan to scan.
The collision cell quadrupole rod assembly (Q2), which always acts as an ion transmission
device, is a quadrupole array of square-profile rods. A variable rf voltage charges the rods,
which creates an electrostatic field that gives stable oscillations to ions in a wide window of
mass-to-charge ratios. An axial field down the length of Q2 speeds throughput.
The collision cell surrounds Q2 and is usually pressurized from about 1 × 10–3 to
4 × 10–3 Torr with argon collision gas. The collision cell is where collision-induced
dissociation takes place.
CID is a process in which an ion collides with a neutral atom or molecule and then, because
of the collision, dissociates into smaller fragments. The mechanism of dissociation involves
converting some of the TKE of the ion into internal energy. This collision places the ion in an
excited state. If the internal energy is sufficient, the ion fragments.
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Mass Analyzers
Quadrupole Offset Voltage
The quadrupole offset voltage is a dc potential applied to the quadrupole rods in addition to
the ramping dc voltage. The offset voltage applied to the two rod pairs of the assemblies is
equal in amplitude and equal in sign. The quadrupole offset voltage accelerates or decelerates
ions and, therefore, sets the TKE of the ions as they enter the quadrupole rod assembly.
In general, for a given experiment, the mass spectrometer has fixed offset voltages for Q1 and
Q2. However, in MS/MS experiments, the quadrupole offset voltage applied to Q3 usually
varies as a scan proceeds. The mass spectrometer automatically computes the necessary Q3
quadrupole offset voltage and then varies the voltage, as appropriate, as each scan proceeds.
The offset voltage applied to Q2 (which contains the collision cell) is responsible for the
collision energy. The collision energy is the difference in potential between the ion source
(where precursor ions are formed) and Q2 (where they collide with collision gas). As the offset
voltage on Q2 increases, the TKE of the precursor ions also increases. As a result, increases in
the Q2 offset voltage increase the energy of ion/Ar collisions. The collision energy is generally
set to one value for an entire scan and can be set from 0 to ±65 V.
Before obtaining any mass spectra, the mass spectrometer tunes Q1 in the Q1MS scan mode
(Q2 and Q3 rf voltage only), and tunes Q3 in the Q3MS scan mode (Q1 and Q2 rf voltage
only). During tuning, the mass spectrometer determines the optimum quadrupole offset
voltage for Q1 and for Q3.
Mass Analyzer Lenses
The mass analyzer has three lens sets. See Figure 24. Those between quadrupoles Q1 and Q2
are designated EL21, EL22, EL23; those between quadrupoles Q2 and Q3 are designated
EL31, EL32, EL33; and the lens between Q3 and the ion detection system is designated as L4
(or the exit lens). All of the lenses have circular holes in their centers through which the ion
beam passes.
The lens assemblies also retain the three rod assemblies to ensure accurate and automatic axial
alignment of the rod assemblies.
The L2x lens set (between quadrupoles Q1 and Q2) and the L3x lens set (between
quadrupoles Q2 and Q3) serve these functions:
• To minimize the amount of collision gas that enters the mass analyzers (Q1 and Q3) from
the collision cell (Q2). (For high-mass transmission, it is important to maintain a low
pressure in the mass analyzers.)
• To retain the collision gas. Lenses EL23 and EL31 form two of the walls of the collision
cell, so they tend to hold the collision gas in the collision cell. However, the collision gas
escapes through the same lens holes through which the ion beam passes.
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Dual-Mode, Discrete-Dynode Ion Detection System
• To prevent gas from entering the mass analyzers. Lenses EL22 and EL21 on one side of
Q2 and lenses L32 and L33 on the other side of Q2 act as baffles to help prevent the gas
that escapes from the collision cell from entering the mass analyzers.
• To shield Q1 from the rf voltage applied to Q2 and vice versa (L2x lens set) and to shield
Q3 from the rf voltage applied to Q2 and vice versa (L3x lens set).
• To focus the ion beam. The three lenses between Q1 and Q2 (and those between Q2 and
Q3) together form a three-element aperture lens. The first and third lenses are generally
set to similar or identical values and the central lens is set to a value different (either
higher or lower) from the other two.
Typically, the voltage applied to the first and third elements of the L2x lens set is somewhat
greater than the quadrupole offset voltage applied to Q1.
In the Q3MS scan mode, the voltage applied to the lenses of the L3x lens set is about the same
as that applied to the corresponding lens in the L2x lens set. However, in the MS/MS scan
modes, the voltage applied to the L3x lens set automatically varies with the quadrupole offset
voltage applied to Q3. As the Q3 quadrupole offset voltage ramps, the voltages applied to the
lenses ramp correspondingly.
Lens L4 is located between Q3 and the ion detection system. L4 is held at ground potential.
Its purpose is to shield Q3 from the high voltage applied to the ion detection system and to
shield the ion detection system from the high rf voltages applied to Q3.
Dual-Mode, Discrete-Dynode Ion Detection System
The TSQ Endura and TSQ Quantiva MSs have a high-sensitivity, dual-mode,
discrete-dynode ion detection system (Figure 17). The ion detection system increases
sensitivity and dynamic range by switching automatically between pulse counting detection
and analog detection. If the ion flux is low, it operates in pulse-counting mode, which
captures every ion event. When the ion flux is high, it switches to analog mode for maximum
dynamic range.
The analog ion detection system includes a high-voltage conversion dynode and an electron
multiplier. Typically, the electron multiplier is set to a gain of about 5 × 105 (that is, for each
ion or electron that enters, 5 × 105 electrons exit) in MS mode and 2 × 106 in MS/MS mode.
The electrometer circuit converts the current that leaves the electron multiplier through the
anode to a voltage, and the data system records the voltage.
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Ion Transmission and Mass Analysis
Dual-Mode, Discrete-Dynode Ion Detection System
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5
Syringe Pump and Divert/Inject Valve
This chapter describes the external syringe pump and divert/inject valve that ship with the
TSQ Endura or TSQ Quantiva mass spectrometer. For information about installing these
components, refer to the TSQ Endura and TSQ Quantiva Getting Connected Guide.
Contents
• Syringe Pump
• Divert/Inject Valve
Syringe Pump
The external Chemyx™ Fusion 100T syringe pump delivers sample solution from an installed
syringe, through the sample transfer line (red PEEK), and into the API source. The motorized
pusher block (Figure 27) depresses the syringe plunger at the flow rate specified in the data
system. (The default flow rate for calibration is 5 μL/min.)
You can start and stop the syringe pump from the data system; refer to the data system Help
for instructions. You can also start and stop the syringe pump by pressing the syringe pump
buttons.
Note If you choose to provide a syringe pump other than the Fusion 100T, ensure that it
can provide a steady, continuous flow of 1–5 μL/min.
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Syringe Pump and Divert/Inject Valve
Divert/Inject Valve
Figure 27. Syringe pump setup (top view)
Teflon™
tubing
LC union,
internal view
Syringe pump
Fingertight
fittings
Red PEEK tubing
Pusher block
Release
knob
Syringe
holder
Syringe
Divert/Inject Valve
The external Rheodyne™ MX Series II™ divert/inject valve is a 6-port motorized valve that
switches between two positions. In the first position, port one connects internally to port two,
port three connects to port four, and port five connects to port six. In the second position, the
valve rotates one position so that port one connects internally to port six, port two connects to
port three, and port four connects to port five. Figure 28 shows the valve’s internal flow paths
for both positions.
The Method Editor in the Xcalibur application identifies the valve’s two positions as “1–2”
(port 1 to 2) and “1–6” (port 1 to 6).
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Syringe Pump and Divert/Inject Valve
Divert/Inject Valve
Figure 28. Divert/inject valve positions
Internal connection path
(light gray)
2
1
2
Port 1 internally switches between port 2
(position 1–2) and port 6 (position 1–6, shown).
1
Valve screw
6
3
4
5
Position 1–2
3
6
4
5
Position 1–6
Configurations
You can configure (plumb) the divert/inject valve as a loop injector (for flow injection
analysis) or as a divert valve. The divert valve can switch the solvent front, gradient endpoint,
or any portion of the LC run to waste. Figure 29 shows both of these configurations.
In the loop injector valve configuration, the valve switches between these two positions:
• Load (position 1–2)—The sample loop is isolated from the solvent stream. Solvent flow
from the LC pump enters and exits the valve through ports five and six, respectively.
When you load the sample into port two, the sample enters and exits the sample loop
through ports one and four, respectively. As you overfill the sample loop, the excess
sample exits the valve through port three to waste.
• Inject (position 1–6)—The sample loop is open to the solvent stream. The solvent flow
from the LC pump flushes sample out of the sample loop, and then exits through port six
into the API source.
In the divert valve configuration, the valve switches between these two positions:
• Detector (position 1–2)—Solvent flow from the LC pump enters the valve through port
five and exits through port six into the API source.
• Waste (position 1–6)—Solvent flow from the LC pump enters the valve through port five
and exits through port four to waste.
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Syringe Pump and Divert/Inject Valve
Divert/Inject Valve
Figure 29. Divert/inject valve plumbed as a loop injector and as a divert valve
Sample input
Sample loop
1
2
6
3
Waste
2
4
1
6
3
4
5
5
API source
API source
Waste
LC pump
LC pump
Loop injector
(Position 1–2 with load configuration)
Divert valve
(Position 1–2 with detector configuration)
Controlling the Divert/Inject Valve
You can control the divert/inject valve as follows:
• Use the mass spectrometer’s data system to specify the parameters in the Divert Valve
Properties pane of the Method Editor. For instructions, refer to the Xcalibur Method
Editor Help.
• Use the valve’s control buttons (Figure 30) to divert the LC flow between the mass
spectrometer and waste when the valve is in the divert valve configuration, or switch
between load and inject modes when the valve is in the loop injector configuration. For
instructions, refer to the manufacturer’s manual.
Figure 30. Divert/inject valve (front view)
Valve position indicator
Six-port, two-position valve
Valve control buttons
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6
System Shutdown, Startup, and Reset
When you are not using the TSQ Endura or TSQ Quantiva system for short periods of time,
place the mass spectrometer in standby mode. For longer periods, for example, two or more
months, you can shut it down completely. In addition, many maintenance procedures for the
system require shutting down the mass spectrometer completely.
Contents
• Shutting Down the System in an Emergency
• Placing the System in Standby Mode
• Turning On the Mass Spectrometer
• Shutting Down the Mass Spectrometer Completely
• Starting the System after a Complete Shutdown
• Resetting the Mass Spectrometer
• Resetting Calibration Parameters
• Restarting the Data System
• On/Off Status for MS Components Under Varying Power Conditions
Shutting Down the System in an Emergency
CAUTION If you must turn off the mass spectrometer in an emergency, turn off the main
power switch located on the right-side power panel (Figure 3). This switch turns off all
power to the mass spectrometer, including the forepump, without harming components
within the instrument. However, do not use this method as part of the standard shutdown
procedure. Instead, see “Shutting Down the Mass Spectrometer Completely.”
To turn off the LC, autosampler, and data system computer in an emergency, use their
respective on/off switch or button.
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System Shutdown, Startup, and Reset
Placing the System in Standby Mode
Placing the System in Standby Mode
If you are temporarily not using the mass spectrometer, for example, from overnight to several
weeks, you do not need to shut it down completely. Instead, place it in standby mode.
 To place the mass spectrometer in Standby mode
1. Complete all data acquisition, if any.
2. On the Windows desktop, click the Tune icon,
(Figure 31).
, to open the Tune window
Figure 31. TSQ Endura Tune window
Three power mode icons
(on/standby/off])
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System Shutdown, Startup, and Reset
Turning On the Mass Spectrometer
3. If your LC/MS system includes an LC pump, turn off the liquid flow to the API source.
For instructions, refer to the LC pump’s manual.
4. In the Tune window, place the mass spectrometer in Standby mode.
The center of the selected power mode icon changes from white to green. The System
LED on the front panel turns yellow. To keep the API source clean, the mass spectrometer
reduces the auxiliary and sheath gas flows to their standby default settings (2 arbitrary).
The mass spectrometer turns off the electron multiplier, conversion dynodes, 8 kV power
to the API source, main rf voltage, and ion optic rf voltages. For a more complete list, see
“On/Off Status for MS Components Under Varying Power Conditions.”
CAUTION Hot surface. Allow heated components to cool to room temperature
(approximately 20 minutes) before you touch or service them.
Turning On the Mass Spectrometer
 To turn on the mass spectrometer
1. Open the Tune window.
2. Click the On icon to place the mass spectrometer in On mode.
The center of the selected power mode icon changes from white to green. The System LED
on the front panel turns green. The high voltage to the electron multiplier turns on.
Shutting Down the Mass Spectrometer Completely
Shut down the TSQ Endura or TSQ Quantiva system completely only when you are not
using it for an extended period of time or when you must shut it down for maintenance or
service. You do not need to shut down the system completely if you are not going to use it
temporarily, such as overnight or through the weekend. Instead, place the system in standby
mode as described in “Placing the System in Standby Mode.”
 To shut down the mass spectrometer completely
1. Follow the procedure, “Placing the System in Standby Mode.”
2. Place the electronics service switch in the Service Mode (down) position.
This turns off the power to the nonvacuum system electronics.
3. Turn off the Main Power switch.
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System Shutdown, Startup, and Reset
Starting the System after a Complete Shutdown
The following occurs:
• All power to the mass spectrometer, including the turbomolecular pumps and the
one or two forepumps, turn off. All LEDs on the front panel are off.
• After approximately 5 seconds, power to the vent valve solenoid shuts off, the vent
valve opens, and the vacuum manifold vents with dry nitrogen. You can hear a
hissing sound.
• After about 2 minutes, the vacuum manifold is at atmospheric pressure.
4. Unplug the mass spectrometer’s power supply cord from the electrical outlet.
CAUTION Do not disconnect the power supply cord from the mass spectrometer
while the other end is still plugged into the electrical outlet.
5. (Optional) Follow the next procedure, “To turn off the LC, gases, data system, and
autosampler.”
Tip If you only plan to perform routine or preventive system maintenance on the mass
spectrometer, the shutdown procedure is now complete. However, if you plan to have the
system off for an extended period of time, Thermo Fisher Scientific recommends that you
follow the next procedure to turn off the LC, gases, data system, and autosampler.
 To turn off the LC, gases, data system, and autosampler
1. If the LC system is included, turn it off as described in the LC manual.
2. Turn off the helium and nitrogen gas supplies at their tanks.
3. Shut down the data system computer and turn off the monitor.
4. If an autosampler and printer are included, use their On/Off switches to turn them off.
Starting the System after a Complete Shutdown
To start the TSQ Endura or TSQ Quantiva system after it has been shut down completely,
follow these procedures:
• Starting the LC (optional)
• Starting the Data System
• Starting the Mass Spectrometer
• Starting the Autosampler (optional)
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Starting the System after a Complete Shutdown
Starting the LC
To start the LC system, follow the startup procedure described in the manufacturer’s manual.
Note Do not turn on the liquid flow to the mass spectrometer until you start the data
system.
Starting the Data System
 To start the data system
Turn on the computer, monitor, and optional printer.
Starting the Mass Spectrometer
Make sure that the data system is running before starting the mass spectrometer. The mass
spectrometer does not operate until it receives instructions from the data system.
 To start the mass spectrometer
1. Turn on the flows for the argon and nitrogen gases at their tanks if they are off.
2. Turn off the Main Power switch and place the electronics service switch in the Service
Mode (down) position.
3. Plug in the power supply cord for the mass spectrometer.
4. Turn on the Main Power switch.
This turns on the forepump and the turbomolecular pumps. All LEDs on the front panel
are off.
5. If the mass spectrometer was turned off for an extended period of time, follow the
procedures in “Pumping Down the Mass Spectrometer,” in Chapter 5 of the TSQ Endura
and TSQ Quantiva Getting Started Guide. Otherwise, wait at least 1 hour to allow the
mass spectrometer to pump down.
6. Place the electronics service switch in the Operating Mode (up) position.
The following occurs:
• The Power LED on the front panel turns green to indicate that the electronics have
power. However, the electron multiplier, conversion dynodes, 8 kV power to the API
source, main rf voltage, and ion optic rf voltage remain off.
• After several more seconds, the Communication LED turns green to indicate that the
mass spectrometer and the data system are communicating. Make sure that the
instrument console window is active. The data system transfers operational software
to the mass spectrometer.
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System Shutdown, Startup, and Reset
Resetting the Mass Spectrometer
• After three minutes, the System LED turns yellow to indicate the software transfer
from the data system to the mass spectrometer is complete and that the mass
spectrometer is in standby mode. When you change the mode from standby to on,
the System LED turns green to indicate that the mass spectrometer is functional and
the high voltages are on.
IMPORTANT On the front panel, the Vacuum LED illuminates green only when
the pressure in the mass analyzer region, as measured by the ionization vacuum
gauge, is below the maximum allowable pressure of 7 × 10–4 Torr.
Although you can calibrate the mass spectrometer after the vacuum LED turns
green, you must allow the mass spectrometer’s vacuum system to stabilize
completely, which takes approximately 15–24 hours of continuous pumping, to
ensure that the calibrations are correct.
Starting the Autosampler
Turn on the autosampler by using its on/off power switch. If necessary, configure the
autosampler. For procedures for placing sample vials, preparing solvent and waste containers,
installing syringes, and so on, refer to the autosampler manual. The TSQ Endura and
TSQ Quantiva Getting Connected Guide provides procedures for connecting the mass
spectrometer to the autosampler by using a contact closure cable.
Resetting the Mass Spectrometer
In the unlikely event that communication is lost between the mass spectrometer and data
system computer, you can reset the mass spectrometer by using the reset button located on the
left-side communications panel.
The following procedure assumes that power to the mass spectrometer and data system
computer are on and that both are operational. If the mass spectrometer, data system
computer, or both are off, see “Starting the System after a Complete Shutdown.”
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Resetting Calibration Parameters
 To reset the mass spectrometer
Hold down the reset button for 3 seconds.
The following occurs:
• The embedded computer restarts. All LEDs on the front panel turn off except the
Power LED.
• After several more seconds, the Communication LED turns green to indicate that the
mass spectrometer and the data system are communicating. The data system transfers
operational software to the mass spectrometer.
• After three minutes, the System LED turns yellow to indicate that the software
transfer from the data system to the mass spectrometer is complete and that the mass
spectrometer is in standby mode. Or, the System LED turns green to indicate that the
mass spectrometer is functional and the high voltages are on.
Resetting Calibration Parameters
If you must reset the calibration parameters to their factory default values, contact your local
Thermo Fisher Scientific service engineer for assistance.
IMPORTANT
• Before resetting the instrument parameters to their default values, make sure that the
system problems you are experiencing are not due to improper API source settings
(such as spray voltage, sheath and auxiliary gas flow, or ion transfer tube temperature).
• If you reset the instrument to the factory calibration settings, always repeat the
calibration of the internal electronic devices as specified in the TSQ Endura and
TSQ Quantiva Getting Started Guide. Otherwise, all instrument calibrations might
produce incorrect results.
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System Shutdown, Startup, and Reset
Restarting the Data System
Restarting the Data System
If possible, use the Windows restart procedure to shut down and restart the data system so
that Windows can properly close applications and save changes to any open Thermo Scientific
application.
Note After you reset the data system, the communications link between the data system
and the mass spectrometer is automatically reestablished. When this occurs, the
Communication LED turns yellow and then green. If the system is unable to reestablish
the communications link, hold down the reset button for 3 seconds.
 To restart the data system by using Windows
1. On the Windows taskbar, choose Start, and then click the arrow next to Shut Down.
2. Choose Restart, and then click OK.
 To restart the data system by using the power button
1. Press the power button on the data system computer.
2. Wait at least 20 seconds after the computer shuts down.
3. Press the power button again.
On/Off Status for MS Components Under Varying Power Conditions
Table 7 summarizes the on/off status of mass spectrometer components, voltages, and API gas
flows.
Table 7. On/Off status of mass spectrometer components, voltages, and API gas flows (Sheet 1 of 2)
Mass spectrometer component
Vent valve
Standby
mode
Off
mode
Closed
Off
Electronics
service switch,
Service Mode position
Main Power switch,
Off (0) position
Closed
Closed
Open
Off
Off
Off
APCI corona discharge needle
Conversion dynode
Electron multiplier
ESI needle
Gas, argon (collision [CID gas])a
Power supply, electron multiplier and
conversion dynode
Vaporizer temperaturea
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6 System Shutdown, Startup, and Reset
On/Off Status for MS Components Under Varying Power Conditions
Table 7. On/Off status of mass spectrometer components, voltages, and API gas flows (Sheet 2 of 2)
Mass spectrometer component
Standby
mode
Off
mode
Electronics
service switch,
Service Mode position
Main Power switch,
Off (0) position
Ion transfer tube dc offset
Ion transfer tube temperature
Mass analyzer, dc offset voltage
Mass analyzer, rf voltage
Off
MP00 and MP0 ion optics, dc offset
voltage
Off
MP00 and MP0 ion optics, rf voltage
RF lens voltage
Embedded computer
Gases, auxiliary, sheath, and
On
Off
sweepb
Gauge, convection vacuum (collision cell)
Gauge, ionization vacuum (mass analyzer)
Fans
On
Forepumps
Gauge, convection vacuum (foreline)
On
Turbomolecular pump and controller
Vent Delay PCB
a
You can control this setting in your method even when the instrument is in standby mode.
b
In standby mode, the Tune application sets the API gases to their standby default settings (2 arbitrary) to keep the API source clean.
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System Shutdown, Startup, and Reset
On/Off Status for MS Components Under Varying Power Conditions
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7
Daily Operation
To ensure the proper operation of the TSQ Endura or TSQ Quantiva system, Thermo Fisher
Scientific recommends that you perform daily preventive maintenance. This chapter specifies
the items to check before operating the system and the cleaning procedures to perform after
completing the analyses.
Contents
• Before Operating the Mass Spectrometer
• After Operating the Mass Spectrometer
Note You do not need to calibrate and tune the mass spectrometer as part of your daily
routine.
Calibration parameters are instrument parameters that affect the mass accuracy and
resolution. Tune parameters are instrument parameters that affect the intensity of the ion
signal. You must tune and calibrate the mass spectrometer (that is, optimize the tune and
calibration parameters) approximately once a quarter. You must optimize the tune
parameters (or change the Tune Method) whenever you change the type of experiment.
To calibrate the instrument and optimize the Tune parameters, refer to the TSQ Endura
and TSQ Quantiva Getting Started Guide.
Before Operating the Mass Spectrometer
Follow these preventive maintenance procedures every day before beginning the first analysis:
• Checking the System Mode
• Checking the Vacuum Pressure Levels
• Checking the Gas Supplies
• Checking the oil level of the forepumps (See “Maintaining the Forepumps” on page 80.)
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Daily Operation
Before Operating the Mass Spectrometer
Checking the System Mode
Make sure that the system is turned on. See “Turning On the Mass Spectrometer.”
Checking the Vacuum Pressure Levels
Before beginning the daily operation of the system, check the vacuum pressure levels and
check for major air leaks. If there is a major air leak, the system does not pump down to
sufficient levels to turn on the system. In the Tune window, a green square,
, indicates that
the readback value is good.
CAUTION For proper performance, operate the TSQ Endura or TSQ Quantiva system at
the proper vacuum levels. Operating the system with poor vacuum levels can cause
reduced sensitivity and reduced electron multiplier life.
You can check the current values of the pressures in the ion transfer tube-rf lens and foreline
(labeled Source Pressure) and in the analyzer region (labeled Analyzer Pressure) in the Status
pane of the Tune window.
 To check the vacuum pressures
1. Open the Tune window.
2. Click the Status tab and click the Expand icon,
, next to Vacuum.
3. Compare the current values of the pressures in the vacuum manifold with the values listed
in Table 8 for the TSQ Endura MS and Table 9 for the TSQ Quantiva MS. If the current
values are higher than normal, you might have an air leak.
Table 8. Typical pressure readings for the TSQ Endura MS
Conditions
Ion source pressure reading
(foreline, ion transfer tube,
S lens region)
Analyzer pressure reading
(analyzer region)
Collision gas off, ion
transfer tube orifice sealed
Less than 0.05 Torr
Less than 6 × 10–6 Torr
(after pumping for at least
12 hours)
Collision gas off, ion
transfer tube orifice open
1.5 Torr
Less than 9 × 10–6 Torr
Collision gas set to
1.5 Torr
1.5 mTorr, ion transfer tube
orifice open
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Approximately
3 × 10–5 Torr
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7 Daily Operation
Before Operating the Mass Spectrometer
Table 9. Typical pressure readings for the TSQ Quantiva MS
Conditions
Source pressure reading
(foreline, ion transfer tube,
rf lens region)
Analyzer pressure reading
(analyzer region)
Collision gas off, ion
transfer tube orifice sealed
Less than 0.05 Torr
Less than 6 × 10–6 Torr
(after pumping for at least
12 hours)
Collision gas off, ion
transfer tube orifice open
3.8–4.2 Torr
Less than 9 × 10–6 Torr
Collision gas set to
3.8–4.2 Torr
1.5 mTorr, ion transfer tube
orifice open
Approximately
3 × 10–5 Torr
If the pressure is high (above 5 × 10–5 Torr in the analyzer region), and you have restarted
the system within the last 30 to 60 minutes, wait an additional 30 minutes and recheck
the pressure. If the pressure is decreasing with time, check the pressure periodically until it
is within the typical pressure range of the mass spectrometer.
If the pressure remains high, your system might have an air leak. If you suspect an air leak,
first inspect the vacuum lines and fittings external to the mass spectrometer for leaks and
take corrective action if necessary. If you suspect an air leak within the mass spectrometer,
contact Thermo Fisher Scientific.
 To check the system for major air leaks
Listen for a rush of air or a hissing sound coming from the mass spectrometer.
Possible causes of a major leak might be a loose or disconnected fitting, an improperly
positioned O-ring, or an open valve.
 To fix an air leak
1. Shut down the system (see Shutting Down the Mass Spectrometer Completely).
2. Visually inspect the vacuum system and vacuum lines for leaks.
3. Check each fitting and flange on the system for tightness, and tighten the fittings or
flanges that are loose.
Do not tighten fittings indiscriminately. Pay particular attention to fittings that have been
changed recently or to fittings that have been subjected to heating and cooling.
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Daily Operation
After Operating the Mass Spectrometer
Checking the Gas Supplies
Check the argon supply on the regulator of the argon gas tank. Make sure that there is
sufficient gas for the analysis. If necessary, replace the tank. Verify that the pressure of argon
gas reaching the mass spectrometer is 135 ±70 kPa (20 ±10 psi). If necessary, adjust the
pressure with the tank pressure regulator.
Check the nitrogen gas supply on the regulator of the nitrogen gas tank or liquid nitrogen
boil-off tank. Make sure that there is sufficient gas for the analysis. Based on 24-hour per day
operation, typical nitrogen consumption is 2800 liters per day (100 ft3/day). If necessary,
replace the tank. Verify that the pressure of nitrogen gas reaching the mass spectrometer is
690 ±140 kPa (100 ±20 psi). If necessary, adjust the pressure with the tank pressure regulator.
For more information about gas requirements, refer to the TSQ Endura and TSQ Quantiva
Preinstallation Requirements Guide.
After Operating the Mass Spectrometer
Follow these preventive maintenance procedures every day after operating the system:
• Flushing the Inlet Components (as needed)
• Purging the Oil in the Forepump
• Emptying the Solvent Waste Container
• Placing the System in Standby Mode
Flushing the Inlet Components
This section describes how to flush the syringe and the inlet components (sample transfer line,
sample tube, and spray insert) at the end of each work day (or more often if you suspect they
are contaminated). You can also use an LC pump to flush the 50:50 methanol/water solution
through the inlet components to the API source at a flow rate of 200–400 μL/min for
approximately 15 minutes.
Tip If a mass spectrum shows unwanted contamination peaks, follow this procedure
whenever needed.
CAUTION When the mass spectrometer’s ion transfer tube is installed, do not flush it with
cleaning solution, which flushes the residue into the mass spectrometer.
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7 Daily Operation
After Operating the Mass Spectrometer
 To flush the inlet components
1. Turn off the liquid flow from the syringe pump.
2. Place the mass spectrometer in Standby mode.
3. Remove the syringe from the syringe pump as follows:
a. Lift the syringe holder off of the syringe.
b. Press the pusher block’s release knob and slide the block to the left.
c. Remove the syringe from the holder.
d. Carefully remove the syringe needle from the Teflon tube on the syringe adapter
assembly.
4. Clean the syringe as follows:
a. Rinse the syringe with a solution of 50:50 methanol/water.
b. Rinse the syringe with acetone several times.
5. Flush the sample transfer line, sample tube, and spray insert as follows:
a. Load the clean syringe with a solution of 50:50 methanol/water (or another
appropriate solvent).
b. Carefully reinsert the syringe needle into the Teflon tube on the syringe adapter
assembly.
c. Slowly depress the syringe plunger to flush the solution through the sample transfer
line, sample tube, and spray insert.
d. Remove the syringe needle from the syringe adapter assembly.
This completes the procedure to flush the inlet components.
Purging the Oil in the Forepump
Purge (decontaminate) the oil in the forepump daily to remove water and other dissolved
chemicals, which can cause corrosion and decrease the lifetime of the forepump. For
instructions, refer to the forepump’s documentation.
The best time to purge the oil is at the end of the working day after you flush the inlet
components. Remember to close the purge valve before continuing normal operation.
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After Operating the Mass Spectrometer
Emptying the Solvent Waste Container
Check the solvent level in the solvent waste container daily. If necessary, empty the container
and dispose of the solvent waste in accordance with local and national regulations.
Placing the System in Standby Mode
After you complete the daily maintenance procedures, place the mass spectrometer in standby
mode as described in “Placing the System in Standby Mode” on page 50.
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8
Maintenance
This chapter provides routine maintenance procedures that you must perform to ensure
optimum performance of the TSQ Endura or TSQ Quantiva system. Optimum performance
depends on maintaining all parts of the instrument on a regular basis. For a list of replaceable
parts, see Chapter 10, “Replaceable Parts.”
Note The following components are slightly different between the TSQ Endura MS and
the TSQ Quantiva MS: sweep cone, ion transfer tube, API source interface, rf lens, MP00
rf lens, and lens L0. Unless otherwise noted, use the TSQ Endura MS procedures.
CAUTION Heavy object. Never lift or move the instrument by yourself; you can suffer
personal injury or damage the instrument.
Contents
• Guidelines
• Maintenance Schedule
• Tools and Supplies
• Maintaining the API Source Housing
• Maintaining the API Source Interface
• Maintaining the Forepumps
• Maintaining the Air Filter
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Maintenance
Guidelines
Guidelines
For optimal results, follow these guidelines when performing the procedures in this chapter:
• Always wear a new pair of lint- and powder-free gloves when handling internal
components. Never reuse gloves after you remove them because the surface contaminants
on them recontaminate clean parts.
• Always place the components on a clean, lint-free work surface.
• Have nearby the necessary tools, supplies, and replacement parts (when applicable).
• Never overtighten a screw or use excessive force.
• Proceed methodically.
IMPORTANT
• Put on a new pair of lint- and powder-free gloves before starting each removal,
cleaning, and reinstallation procedure.
• Make sure that you do not introduce any scratches or surface abrasions while
handling the API source interface components. Even small scratches can affect
performance if they are close to the ion transmission path. Avoid using tools, such as
metal pliers, that might scratch these components.
Maintenance Schedule
Table 10 lists the system maintenance procedures, their location in or outside this manual,
and their recommended frequency.
Table 10. Mass spectrometer maintenance procedures and frequency (Sheet 1 of 2)
MS component
Procedure
Recommended frequency
API source
Flush (clean) the sample transfer
line, sample tube, and spray insert.
Daily
As neededa
Replace the APPI lamp.
66
Replace the H-ESI needle insert.
If the metal needle is obstructed
Replace the APCI fused-silica
tubing.
If the tubing is obstructed
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page 69
Clean the API source housing.
Clean the APPI fan filter.
Reference
Ion Max NG and
EASY-Max NG
Ion Sources User
Guide
Thermo Scientific
8 Maintenance
Maintenance Schedule
Table 10. Mass spectrometer maintenance procedures and frequency (Sheet 2 of 2)
MS component
Procedure
API source interface
Clean the ion sweep cone and spray Daily, or more often depending on
cone.
analytical conditions
Forepump (each)
Cooling fans
Recommended frequency
Remove and clean the ion transfer
tube.
Weekly, or if the ion transfer tube
bore is contaminated or
obstructed
Replace the ion transfer tube.
If the bore becomes corroded or
blocked
Clean the exit lens or rf lens.
As needed, depending on
analytical conditions
Clean multipole MP00 rf lens and
lens L0.
As needed, depending on
analytical conditions
Clean quadrupole Q00
During skimmer and tube lens
cleaning*
Purge (decontaminate) the oil and
check for leaks.
Daily
Add oil.
As needed, based on oil level
Change the oil.
Every 12 months of typical use, or
if the oil is cloudy or discolored
Clean the air filter.
Every 4 months
Reference
page 70
Manufacturer’s
manual
page 80
For instructions about maintaining the LC modules, refer to that instrument’s manual.
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Maintenance
Tools and Supplies
Tools and Supplies
The mass spectrometer requires very few tools to perform routine maintenance procedures.
You can remove and disassemble many of the components by hand. Table 11 lists the
necessary chemicals, tools, and equipment for maintaining the instrument. (One of the tools
is in the TSQ Source Installation Kit.) In addition, you can use the contents of the PM
Cleaning Kit (P/N 70111-62112).
CAUTION Avoid exposure to potentially harmful materials.
By law, producers and suppliers of chemical compounds are required to provide their
customers with the most current health and safety information in the form of Material
Safety Data Sheets (MSDSs) or Safety Data Sheet (SDS). The MSDSs and SDSs must be
freely available to lab personnel to examine at any time. These data sheets describe the
chemicals and summarize information on the hazard and toxicity of specific chemical
compounds. They also provide information on the proper handling of compounds, first
aid for accidental exposure, and procedures to remedy spills or leaks.
Read the MSDS or SDS for each chemical you use. Store and handle all chemicals in
accordance with standard safety procedures. Always wear protective gloves and safety
glasses when you use solvents or corrosives. Also, contain waste streams, use proper
ventilation, and dispose of all laboratory reagents according to the directions in the MSDS
or SDS.
Table 11. Chemicals, tools, and equipment (Sheet 1 of 2)
Description
Part number
Chemicals
Acetone, LC/MS-grade
Fisher Scientific™ AX0120-2
Detergent (for example, Liquinox™)
(Liquinox) Fisher Scientific:
• 50-821-299 (1 quart)
• 50-821-298 (1 gallon)
Methanol, LC/MS-grade
Fisher Scientific A456-1
Nitrogen gas, clean and dry
–
Water, LC/MS-grade
Fisher Scientific W6-1
Tools
Ion transfer tube removal toolsa
• TSQ Endura MS
• TSQ Quantiva MS
68
70111-20258
70005-20972
Screwdriver, Phillips #2 (M3)
–
(Optional) Toothbrush, soft (or similar tool)
–
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8 Maintenance
Maintaining the API Source Housing
Table 11. Chemicals, tools, and equipment (Sheet 2 of 2)
Description
Part number
(Optional) Tweezers, plastic (or similar tool)
–
Equipment
Beaker or graduated cylinder (for use with
methanol)
–
Chamois-tipped swabs
00725-01-00028
Gloves, lint-free and powder-free
Fisher Scientific 19-120-2947b
Unity Lab Services:
• 23827-0008 (size medium)
• 23827-0009 (size large)
Industrial tissues, lint-free
–
Magnification device
–
MICRO-MESH™ polishing swabs, 6000 grit
(light purple color), 2.25 in. long
00725-01-00027
Sonicator
–
a
Provided in the TSQ Source Installation Kit
b
Multiple sizes are available.
Maintaining the API Source Housing
Only Thermo Fisher Scientific service engineers can service the API source housing, while
user maintenance is limited to cleaning the housing as necessary. Follow all safety precautions
in the Ion Max NG and EASY-Max NG Ion Sources User Guide regarding the installation and
removal of the API source. For any additional service, contact your local Thermo Fisher
Scientific service engineer.
 To clean the API source housing
1. After the API source cools to room temperature, remove it from the mass spectrometer.
2. Put on appropriate eye-wear and gloves.
3. In an appropriate fume hood, rinse the interior of the housing with LC/MS-grade
methanol.
4. Allow the housing to dry before you install it on the mass spectrometer.
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Maintenance
Maintaining the API Source Interface
Maintaining the API Source Interface
While you or the service engineer can remove and service the API source interface, only the
service engineer may service the other internal components.
To maintain the API source interface, follow these procedures:
• Cleaning the Ion Sweep Cone, Spray Cone, and Ion Transfer Tube
• Removing the API Source Interface
• Cleaning the RF Lens, Exit Lens, MP00 RF Lens, and Lens L0
• Reinstalling the API Source Interface
Note Before you continue, read the precautions in “Cautions and Special Notices” on
page xv.
IMPORTANT
• Prepare a clean work surface by covering the area with lint-free paper.
• Put on a new pair of lint- and powder-free gloves before starting each of these
removal, cleaning, and reinstallation procedures.
Cleaning the Ion Sweep Cone, Spray Cone, and Ion Transfer Tube
Because buffer salts or high concentrations of sample can cause blockages, you must clean the
bore of the ion transfer tube. If pressure in the ion transfer tube and rf lens region (as
measured by the Source Pressure gauge) drops considerably below 1 Torr, a blocked ion
transfer tube is likely the cause.
Tip You do not have to vent the system to remove the ion transfer tube.
Follow these procedures:
1. To remove the ion transfer tube
2. To clean the spray cone and O-ring
3. To clean the ion transfer tube
4. To clean the ion sweep cone
 To remove the ion transfer tube
CAUTION Hot surface. The external surface of the spray insert and API source
housing can become hot enough to burn your skin. Before you touch or remove
heated parts, allow the part to cool to room temperature (approximately 20 minutes)
before you touch it.
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Maintaining the API Source Interface
1. If your LC/MS system includes an LC pump, turn off the liquid flow to the API source.
For instructions, refer to the LC pump’s manual.
2. Place the mass spectrometer in Off mode.
You can observe the readback temperature for the ion transfer tube on the Ion Source
page in the Ion Source pane.
3. Place the mass spectrometer’s electronics service switch in the Service Mode (down)
position to turn off the nonvacuum system voltages.
The electronics service switch is located on the right side of the instrument.
CAUTION To avoid an electric shock, make sure that the electronics service switch is
in the Service Mode (down) position before proceeding.
4. After the API source cools to room temperature, remove it.
5. Remove the ion sweep cone by grasping its outer ridges and pulling it off of the API cone
seal (Figure 32).
CAUTION
• Make sure that you do not accidentally lift the release lever located at the top of
the API source interface, which will vent the mass spectrometer.
• To avoid contaminating the ion transfer tube, do not touch its exposed entrance.
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Maintenance
Maintaining the API Source Interface
Figure 32. Ion sweep cone removed from the MS mount assembly
Release lever for the
API source interface
API cone seal
Ion sweep cone
6. To remove the ion transfer tube, do one of the following:
• (TSQ Endura MS) Align the flat edges (hook) of the custom removal tool with the
flat edges on the exposed tip of the ion transfer tube (Figure 33), and then rotate the
tool counterclockwise. When the tube is free of the spray cone, use the hook on the
tool to pull it straight out of the API source interface.
Figure 33. Ion transfer tube removal tool (TSQ Endura MS)
API source interface
Fit this end of the tool around the
exposed ion transfer tube.
–or–
• (TSQ Quantiva MS) Turn the ion transfer tube with the custom removal tool
(Figure 34) until you can pull it free from the API source interface.
Tip If necessary, insert a hex key through a side hole for leverage.
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Maintaining the API Source Interface
Figure 34. Ion transfer removal tool (TSQ Quantiva MS)
 To clean the spray cone and O-ring
Note The TSQ Quantiva MS does not have an O-ring behind its ion transfer tube.
1. Soak the lint-free tissues or chamois-tipped swabs in a 50:50 solution of methanol/water,
and then clean the exterior surface of the spray cone.
2. (TSQ Endura MS) Remove and inspect the O-ring located in the spray cone under the
entrance end of the ion transfer tube (Figure 35).
Figure 35. Spray cone, O-ring, ion transfer tube, and ion sweep cone (TSQ Endura MS)
API cone seal
Spray cone
Vespel™ O-ring
Ion transfer tube
Gas inlet on the ion
sweep cone
3. (TSQ Endura MS) Clean the O-ring with methanol or replace it if necessary.
4. Using a magnification device, inspect the components for any residual lint or particulates.
Note Inspect the inside surfaces and edges to confirm that no lint or particulates are
present. Use plastic tweezers or a similar tool to remove the lint or particulate.
5. (TSQ Endura MS) Reinstall the O-ring in the spray cone.
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Maintaining the API Source Interface
 To clean the ion transfer tube
IMPORTANT Always use LC/MS-grade methanol and LC/MS-grade water.
1. For 10 minutes, soak the component in a 50:50 solution of methanol/water to remove
contaminants.
2. Sonicate the component in water for 10 minutes.
3. Dry the component with nitrogen gas to make sure that all the solvent evaporates.
Replace the ion transfer tube if the bore becomes corroded or blocked.
4. Reinstall the ion transfer tube into the heater block, as follows:
CAUTION Take these precautions when reinstalling the ion transfer tube:
• Put on a new pair of lint- and powder-free gloves.
• Verify that everything is properly aligned to prevent stripping the threads on the
ion transfer tube.
• Do not bend the ion transfer tube. Rotate it as you insert it.
 To clean the ion sweep cone
1. Soak lint-free tissues or chamois-tipped swabs in a 50:50 solution of methanol/water, and
then clean both sides of the ion sweep cone.
2. For 10 minutes, sonicate the component in either a 50:50 solution of methanol/water or
a 1% solution of Liquinox in water.
3. Rinse the component thoroughly with water.
4. Sonicate the component in water for 10 minutes.
5. Sonicate the component in methanol for 10 minutes.
6. Rinse the component with methanol.
7. Dry the component with nitrogen gas to make sure that all the solvent evaporates.
8. Using a magnification device, inspect the component for any residual lint or particulates.
After you clean and reinstall these components, turn on the nonvacuum system voltages by
placing the mass spectrometer's electronics service switch in the Operating Mode (up)
position.
Tip If you successfully unblocked the ion transfer tube, check that the Source Pressure
reading has increased to a normal value (below 2 Torr for the TSQ Endura MS or below
4.5 Torr for the TSQ Quantiva MS). If trying this method does not clear the blockage,
replace the ion transfer tube.
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Maintaining the API Source Interface
Removing the API Source Interface
 To remove the API source interface
CAUTION To avoid an electrical shock, be sure to follow the instructions in “Shutting
Down the Mass Spectrometer Completely” on page 51 before continuing with this
procedure.
1. Shut down and vent the system, and let it cool to room temperature.
Venting the mass spectrometer can take several minutes.
CAUTION Hot surface. Allow heated components to cool to room temperature
(approximately 20 minutes) before you touch or service them.
2. Unplug the mass spectrometer’s power supply cord from the electrical outlet.
CAUTION Do not disconnect the power supply cord from the mass spectrometer
while the other end is still plugged into the electrical outlet.
3. Remove the API source housing.
4. Lift up the release latch, grasp the API source interface with your fingers, and then
carefully pull it out of the vacuum manifold (Figure 36).
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Maintenance
Maintaining the API Source Interface
Figure 36. API source interface removed from the vacuum manifold (TSQ Endura MS)
Vacuum manifold
Release latch on
the API source
interface
Viton™ O-ring
Cleaning the RF Lens, Exit Lens, MP00 RF Lens, and Lens L0
Chemicals can accumulate on the surfaces of the rf lens, exit lens, MP00 rf lens, and lens L0.
However, the use of an rf lens that incorporates an rf electric field minimizes the harmful
effects of this contamination. The lenses require cleaning less often than the ion sweep cone
and the ion transfer tube. How frequently you clean these lenses depends on the type and
quantity of the compounds that you analyze. Remove the lenses from the API source interface
cage before cleaning them. No tools are needed to remove or install these components.
To clean the rf lens, exit lens, MP00 rf lens, and lens L0, follow these procedures:
1. To remove the rf lens, exit lens, MP00 rf lens, and lens L0
2. To clean the rf lens, exit lens, MP00 rf lens, and lens L0
3. To reinstall the rf lens, exit lens, multipole MP00, and lens L0
4. To reinstall the API source interface
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Maintaining the API Source Interface
 To remove the rf lens, exit lens, MP00 rf lens, and lens L0
1. Remove the API source interface (see page 75).
2. Wearing clean, lint- and powder-free gloves, loosen and extend the two captive
thumbscrews that secure the rf lens, exit lens, multipole MP00, and lens L0 to the cage.
3. Pull the multipole MP00 and lens L0 assembly off of the API source interface cage. See
Figure 37. Place them on a clean, lint-free surface.
Figure 37. Removing the multipole MP00 and lens L0 assembly
API source interface cage
Retainer thumbscrews
loosened and extended
Lens L0
Multipole MP00 and
lens L0 assembly
4. Grasp the two retainer thumbscrews and carefully pull the rf lens (Figure 38) with the exit
lens straight out of the API source interface cage.
5. Remove the exit lens off of the rf lens. Place both on a clean surface.
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Maintenance
Maintaining the API Source Interface
Figure 38. Removing the rf lens and exit lens (TSQ Endura MS)
RF lens and exit lens assembly
Exit lens
6. Remove multipole MP00 and lens L0 by pushing them out of the MP00-L0 mount cage.
Place them on a clean surface.
Figure 39. Removing the lens L0 and multipole MP00 from the MP00-L0 mount cage
Lens L0
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MP00 rf lens
Multiple MP00
Thermo Scientific
8 Maintenance
Maintaining the API Source Interface
 To clean the rf lens, exit lens, MP00 rf lens, and lens L0
CAUTION Do not clean the lenses with abrasives, acidic or caustic substances, or
detergents not specified in this chapter.
IMPORTANT Always use LC/MS-grade methanol and LC/MS-grade water.
1. Using a magnification device, inspect the components for any lint, particulates, and
sample buildup or coatings.
2. For 10 minutes, sonicate the components in either a 50:50 solution of methanol/water or
a 1% solution of Liquinox in water.
3. If a sonicator is not available, do the following:
• To clean the rf lens, use chamois-tipped swabs with a 1% solution of Liquinox in
water. To clean the areas that you cannot reach with the swab, use the 6000 grit
MICRO-MESH polishing swabs.
• To clean the exit lens, use a soft toothbrush with a 1% solution of Liquinox in water.
4. For the exit lens, MP00 rf lens, and lens L0, use the 6000 grit MICRO-MESH polishing
swabs to clean the bore.
5. Rinse the components thoroughly with water.
6. Sonicate the components in water for 10 minutes.
7. Sonicate the components in methanol for 10 minutes.
8. Rinse the components with methanol.
9. Dry the components with nitrogen gas to make sure that the solvent evaporates.
10. Using a magnifying device, inspect the components for any residual lint or particulates.
Note Inspect the orifices to confirm that no lint or particulates are present in the bore
of the orifices. Use plastic tweezers or a similar tool to remove the lint or particulate.
 To reinstall the rf lens, exit lens, multipole MP00, and lens L0
1. Attach the exit lens to the rf lens, and then reinsert the rf lens into the API source
interface cage (Figure 38).
2. Reassemble the multipole MP00 and lens L0 assembly.
3. Attach the MP00-L0 assembly to the API source interface cage, and then attach lens L0
(Figure 37).
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8
Maintenance
Maintaining the Forepumps
Reinstalling the API Source Interface
 To reinstall the API source interface
1. Orient the API source interface with the release latch at the top (Figure 36).
2. Carefully insert the API source interface into the vacuum manifold.
3. Reinstall the API source housing.
4. Start up the system as described in “Starting the System after a Complete Shutdown” on
page 52.
Maintaining the Forepumps
Maintaining the forepumps requires inspecting, adding, purging, and changing the pump oil.
Refer to the manufacturer’s manual for instructions.
Check the forepump oil often. New oil has a translucent light amber color. During normal
operation, oil must always be visible in the oil level sight glass between the MIN and MAX
marks. If the oil level is below the MIN mark, add oil. If the oil is cloudy or discolored, purge
the oil to decontaminate dissolved solvents. If the pump oil is still discolored, change it. Plan
to change the pump oil every 10 000 hours (or about every 12–13 months) of operation.
CAUTION To minimize the risk of oil contamination in the vacuum system, make sure
that the purging ballast is closed when you vent the system to atmosphere.
Maintaining the Air Filter
Clean the air filter located behind the mass spectrometer’s front cover every four months, or
sooner if it is dirty.
 To clean the air filter
Note You do not need to remove the API source to remove the front cover of the mass
spectrometer.
1. Remove the air filter as follows:
a. Remove the front cover of the mass spectrometer as follows:
i.
Disconnect the plumbing tubing to the API source.
ii. Depress the four spring catches that are located on either side of the front cover.
iii. Pull the front cover off at an angle to clear the API source.
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8 Maintenance
Maintaining the Air Filter
b. Remove the filter from the filter bracket (Figure 40).
Figure 40. Air filter location in the mass spectrometer with the front cover removed
Air filter
Spring catches
Spring catches
2. Wash the air filter in a solution of soap and water.
3. Rinse the filter with tap water, and then allow it to air dry.
4. Reinstall the air filter and front cover.
5. Reconnect the plumbing tubing.
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Maintenance
Maintaining the Air Filter
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9
Diagnostics and PCB and Assembly Replacement
The TSQ Endura and TSQ Quantiva system diagnostics can test many instrument
components. For example, the diagnostics can help you locate a problem with the instrument
electronics. Usually, replacing a faulty PCB or assembly can correct the problem. After
applying the fix, run the diagnostic tests again to verify that the instrument is functioning
properly.
Contents
• Running the System Diagnostics
• Replacing Fuses, PCBs, and Power Supplies
Running the System Diagnostics
The system diagnostics test the major electronic circuits within the mass spectrometer and
indicate whether the circuits pass or fail the tests.
The system diagnostics do not diagnose problems that are not electrical in nature. For
example, they do not diagnose poor sensitivity due to misaligned or dirty components or to
improper tuning. Therefore, the person running the diagnostics must be familiar with system
operation and basic hardware theory as well as the details of the diagnostics.
Typically, only a Thermo Fisher Scientific service engineer runs diagnostic tests because
certain tests can overwrite system parameters. However, before calling a service engineer to
run diagnostics, consider these questions:
• Did the system fail when you were running samples?
• Did problems occur after you performed maintenance on the instrument, data system, or
peripherals?
• Did you change the configuration of the system, cables, or peripherals just before the
problem occurred?
If the answer is yes to the first item above, there is the possibility of a hardware failure, and
running the diagnostics is appropriate.
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9
Diagnostics and PCB and Assembly Replacement
Replacing Fuses, PCBs, and Power Supplies
If the answer is yes to either of the last two questions above, the problem is probably
mechanical, not electrical. Verify again that alignment, configurations, and cable connections
are correct before you call the service engineer. Keep careful notes documenting the nature of
the problem and the corrective steps you have taken. If you are not successful in correcting the
problem, you can email this information to your field service engineer. The Field Service
department can then do a preliminary evaluation of the problem before an engineer arrives at
your site.
Note A subset of the diagnostic tools targets specific functions of the entire mass
spectrometer. In general, these system evaluation tools do not contain pass or fail criteria
nor do they rate the performance. Instead, they provide data that can be interpreted by a
service engineer. Because the system evaluations examine complex interactions, the service
engineer uses the data in conjunction with other tools and tests to form a diagnosis.
 To run diagnostics
Note Some diagnostic tests require that you infuse calibration solution.
1. Open the Tune window.
2. Click the Diagnostics icon (lower left corner) to open the Diagnostics pane.
3. Select which diagnostics you want to run and click Start.
The data system displays the status of the diagnostics in the Tune window.
Replacing Fuses, PCBs, and Power Supplies
Fuses protect the various circuits by opening whenever an overcurrent condition occurs. On
the mass spectrometer, an open fuse indicates a failed board or electronic module that a
service engineer must replace.
The electronic assemblies that control the operation of the mass spectrometer are distributed
among various PCBs and other modules located in the tower, in the embedded computer, and
on or around the vacuum manifold of the mass spectrometer.
CAUTION Thermo Fisher Scientific service is required. Because the electronic
assemblies are close-packed to minimize the size of the instrument, only a service engineer
can replace electrical components (that is, fuses, PCBs, power supplies, and so on).
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10
Replaceable Parts
This chapter provides the kit part numbers for the TSQ Endura and TSQ Quantiva MSs.
Note You receive all of the listed kits with your ordered system, except for the
TSQ Chemical Kit. This arrives separately as part of the preinstallation kit.
Contents
• TSQ Chemical Kit
• Calibration Kit
• MS Setup Kit
• Performance Specification Kit
• Single Mechanical Pump Kit
• Dual Mechanical Pumps Kit
• TSQ Source Installation Kit
• API Source Interface
• Miscellaneous Parts
TSQ Chemical Kit
TSQ Chemical Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80100-62006
Reserpine Solution Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80100-62033
Triple quad calibration solution, polytyrosine 1-3-6, 10 mL
(Pierce™ 88325) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00301-22924
LCMS Functionality Test Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . HAZMAT-01-00044
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10 Replaceable Parts
Calibration Kit
Calibration Kit
Calibration Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80000-62013
Source LC Connection Kit (Table 12) . . . . . . . . . . . . . . . . . . . . . . . . . . . 80000-62057
Syringe, gas tight, 500 μL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00301-19016
Syringe Adapter Kit (Table 13) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70005-62011
Table 12. Source LC Connection Kit (P/N 80000-62057)
Item
Part number
Fitting, fingertight, two-piece, one wing, 10-32
(Upchurch Scientific™ F-200, 2 provided)
00101-18195
Grounding union, zero-dead-volume (ZDV), stainless steel,
1/16 in. orifice, 0.010 in. (0.25 mm) thru-hole, 10-32
(Upchurch Scientific U-435)
00101-18182
Tubing, natural PEEK, 1/16 in. OD, 0.0025 in. ID, 28 cm
(11 in.) long
80000-22032
Tubing, red PEEK, 1/16 in. OD, 0.005 in. ID, 18 cm (7.1 in.)
long (2 provided)
80000-22053
Table 13. Syringe Adapter Kit (P/N 70005-62011)
Item
Ferrule, fingertight, natural PEEK
(Upchurch Scientific F-142, 2 provided)
Fitting, fingertight, one-piece, natural PEEK, 10-32
(Upchurch Scientific F-120, 16 provided)
86
Part number
00101-18196
00109-99-00016
Fitting, fingertight, two-piece natural PEEK, two wings, 10-32
(Upchurch Scientific F-300, 2 provided)
00101-18081
Tubing, red PEEK, 1/16 in. OD, 0.005 in. ID, 0.6 m (2 ft) long
(Upchurch Scientific 1535XL)
00301-22912
Tubing, Teflon FEP, 1/16 in. OD, 0.030 in. ID, 3 cm (1.2 in.)
long (Upchurch Scientific 1522)
00301-22915
Union, HPLC, black PEEK, 10-32, 0.01 in. thru-hole
(Upchurch Scientific P-742)
00101-18202
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Thermo Scientific
10
Replaceable Parts
MS Setup Kit
MS Setup Kit
MS Setup Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80100-62003
Drain hose adapter with 0-ring . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70111-20971
Connector plug, MINI-COMBICON™, 8-pin, 26.67 mm (1.05 in.) long,
rated 160 V, 8 A (contact closure, 2 provided) . . . . . . . . . . . . . . . . . . 00004-21512
Container, Nalgene™, 4 L heavy-duty; filling/venting cap . . . . . . . . . . . . . 80100-20265
Ethernet cables, shielded Category 5e, 2.1 m (7 ft) long
(2 provided) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00302-99-00036
Ethernet power supply (rated 100–240 Vac, 50/60 Hz, 0.6/0.3 A input;
18 W, 12 Vdc, 1.5 A output) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00012-01-00039
Ethernet switch, 5-port Gigabit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00825-01-00111
Ferrule, brass, front, 1/4 in. ID (2 provided). . . . . . . . . . . . . . . . . . . . . . . 00101-10000
Ferrule, brass, front, 1/8 in. ID (2 provided). . . . . . . . . . . . . . . . . . . . . . . 00101-08500
Ferrule, brass, back, 1/4 in. ID (2 provided) . . . . . . . . . . . . . . . . . . . . . . 00101-04000
Ferrule, brass, back, 1/8 in. ID (2 provided) . . . . . . . . . . . . . . . . . . . . . . 00101-02500
Swagelok™-type nut, brass, 1/4 in. ID (2 provided). . . . . . . . . . . . . . . . . . 00101-12500
Swagelok-type nut, brass, 1/8 in. ID (2 provided). . . . . . . . . . . . . . . . . . . 00101-15500
Tubing, precleaned copper, 1/8 in. OD, 0.030 in. thick, 4.6 m (15 ft)
long (for the UHP argon and nitrogen gases) . . . . . . . . . . . . . . . . . . . 00301-22701
Tubing, Teflon PFA, 1/4 in. (6.35 mm) OD, 0.062 in. (1.57 mm)
thick, 4.6 m (15 ft) long (for the HP nitrogen gas). . . . . . . . . . . . . . . 00101-50100
Tubing, Tygon™, 1-3/8 in. OD, 1 in. ID, 3 m (10 ft)
(for the drain/waste line) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00301-01-00020
Performance Specification Kit
Performance Specification Kit. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80100-62008
Column, HPLC, 20 × 2.1 mm ID, Hypersil GOLD AQ™ C18,
1.9 μm particles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00109-01-00013
Fitting, fingertight, one-piece, natural PEEK, 10-32
(Upchurch Scientific F-120, 10 provided) . . . . . . . . . . . . . . . . . . .00109-99-00016
Needle port, PEEK (Rheodyne 9013). . . . . . . . . . . . . . . . . . . . . . . . . . . . 00110-22030
Sample loop, 2 μL, PEEK . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00110-16012
Syringe, gas tight, 500 μL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00301-19016
Tubing, red PEEK, 1/16 in. OD, 0.005 in. ID, 3 m (10 ft) long
(Upchurch Scientific 1535XL) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00301-22912
Union Tee, HPLC, PEEK, 1/16 in. orifice, 0.020 in. (0.5 mm) thru-hole,
10-32 (provided with fingertight fittings)
(Upchurch Scientific P-727) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00101-18204
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10 Replaceable Parts
Single Mechanical Pump Kit
Single Mechanical Pump Kit
Single Mechanical Pump Kit. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80100-62004
Forepump, Oerlikon Leybold Vacuum™, SOGEVAC™ SV 65 BI,
single-phase 230 Vac, 50/60 Hz . . . . . . . . . . . . . . . . . . . . . . . . . . 00108-01-00032
Accessories Single Mechanical Pump Kit (Table 14) . . . . . . . . . . . . . . . . . 80100-62015
Table 14. Accessories Single Mechanical Pump Kit (P/N 80100-62015)
Item
90-Degree Elbow Installation Kit (2 provided, Table 15)
Part number
97055-62036S
Relay control cable, single pump, 2.4 m (8 ft) long (preassembled)
80000-63139
Single pump vacuum hose assembly, KF40, 2.4 m (8 ft) long
(preassembled)
80000-60229
Tubing, Tygon, 3/4 in. (19.1 mm) OD, 0.5 in. (12.7 mm) ID, 3 m
(10 ft) long
00301-22920
Table 15. 90-Degree Elbow Installation Kit (P/N 97055-62036S)
Item
Part number
Centering ring with O-ring, nitrile and aluminum, NW40
00108-02-00005
Elbow, aluminum, NW40, 90 degree
00108-02-00010
Swing clamp, aluminum, NW32/40
00108-02-00004
Dual Mechanical Pumps Kit
Dual Mechanical Pumps Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80100-62013
Forepump, Oerlikon Leybold Vacuum, SOGEVAC SV 65 BI,
single-phase 230 Vac, 50/60 Hz (2 provided) . . . . . . . . . . . . . . . . 00108-01-00032
Accessories Dual Mechanical Pump Kit (Table 16) . . . . . . . . . . . . . . . . . . 80100-62016
Table 16. Accessories Dual Mechanical Pump Kit (P/N 80100-62016)
Item
90-Degree Elbow Installation Kit (3 provided, Table 15)
97055-62036S
Dual relay control cable, 2.4 m (8 ft) long (preassembled)
80100-63146
Dual pump vacuum hose assembly (preassembled)
80100-60049
Fitting Tee, barbed, nylon, for 0.5 in. (12.7 mm) ID tubing
Tubing, Tygon, 3/4 in. (19.1 mm) OD, 0.5 in. (12.7 mm) ID, 6 m
(20 ft) long
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00103-01-00012
00301-22920
Thermo Scientific
10 Replaceable Parts
TSQ Source Installation Kit
TSQ Source Installation Kit
TSQ Source Installation Kit
Ion transfer tube removal tool, TSQ Endura. . . . . . . . . . . . . . . . . . . . . . . 70111-20258
Ion transfer tube removal tool, TSQ Quantiva . . . . . . . . . . . . . . . . . . . . . 70005-20972
L0 lens removal tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70005-20900
Viper™ Capillary Kit (5 provided). . . . . . . . . . . . . . . . . . . . . . . . . . . . 00109-99-00068
API Source Interface
TSQ Endura MS
API source interface assembly
Exit lens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Ion sweep cone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Ion transfer tube . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Lens L0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
O-ring, Vespel, graphite, 0.325 in. ID, 0.046 in. thick
(under ion transfer tube). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
SRIG lens stack (S-lens) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
80100-20070
80000-20895
70005-20606
80100-20548
97055-20442
80000-60136
TSQ Quantiva MS
API source interface assembly
Exit lens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Ion sweep cone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Ion transfer tube (vertical orifice) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Lens L0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
SRIG lens stack (ion funnel) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
80100-20070
80100-20646
80100-20641
80100-20548
80100-60036
Miscellaneous Parts
Divert/Inject Valve and Syringe Pump Assembly
Divert/inject valve, Rheodyne MX Series II. . . . . . . . . . . . . . . . . . . . . . . . 00109-99-00046
Holder, divert valve and syringe pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80000-60363
Syringe pump, Chemyx Fusion 100T . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00109-99-00045
Air Filter
Air filter, metal mesh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80000-10355
Forepump Accessories
Internal demister (exhaust) filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00108-01-00041
Lubricant oil, 1 L . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . HAZMAT-01-00063
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10 Replaceable Parts
Miscellaneous Parts
Power Supply Cords
Mass Spectrometer
North American locations: NEMA 6-15 plug, rated 250 Vac, 15 A,
2.5 m (8 ft) long . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96000-98035
International locations: CEE (3-pole) plug, rated 250 Vac, 16 A,
2.5 m (8 ft) long . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80000-63188
Forepump
North American locations: NEMA 6-15 plug, rated 250 Vac, 15 A,
2.5 m (8 ft) long . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Provided with the forepump
International locations: CEE (3-pole) plug, rated 250 Vac, 16 A,
2.5 m (8 ft) long . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80000-63186
Sample Loop
2 μL, Peek . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00110-16012
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G
Glossary
A
B
C
D
E
F
G
H
I
J
K
L M N O
A
API ion transfer tube A tube assembly that assists in
desolvating ions that are produced by the ESI, APCI,
or NSI nozzle.
API ion transfer tube offset voltage A dc voltage
applied to the ion transfer tube. The voltage is
positive for positive ions and negative for negative
ions.
API source The sample interface between the liquid
chromatograph (LC) and the mass spectrometer
(MS).
API stack Consists of the components of the API
source that are held under vacuum and includes the
ion spray cone, ion transfer tube, exit lens, and ion
transfer tube mount.
atmospheric pressure chemical ionization (APCI) A
soft ionization technique done in an ion source
operating at atmospheric pressure. Electrons from a
corona discharge initiate the process by ionizing the
mobile phase vapor molecules. A reagent gas forms,
which efficiently produces positive and negative ions
of the analyte through a complex series of chemical
reactions.
atmospheric pressure ionization (API) Ionization
performed at atmospheric pressure by using
atmospheric pressure chemical ionization (APCI),
heated-electrospray (H-ESI), or nanospray ionization
(NSI).
Thermo Scientific
P
Q
R
S
T
U
V W X
Y
Z
atmospheric pressure photoionization (APPI) A
soft ionization technique that shows an ion generated
from a molecule when it interacts with a photon
from a light source.
auxiliary gas The outer-coaxial gas (nitrogen) that
assists the sheath (inner-coaxial) gas in dispersing
and/or evaporating sample solution as the sample
solution exits the ESI or APCI (optional) spray
insert.
C
centroid data Data used to represent mass spectral
peaks in terms of two parameters: the centroid (the
weighted center of mass) and the intensity. The data
is displayed as a bar graph. The normalized area of
the peak provides the mass intensity data.
charge state The imbalance between the number of
protons (in the nuclei of the atoms) and the number
of electrons that a molecular species (or adduct ion)
possesses. If the species possesses more protons than
electrons, its charge state is positive. If it possesses
more electrons than protons, its charge state is
negative.
collision energy The energy used when ions collide
with the collision gas.
collision gas A neutral gas used to undergo collisions
with ions.
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Glossary: collision-induced dissociation (CID)
collision-induced dissociation (CID) A method of
fragmentation where ions are accelerated to highkinetic energy and then allowed to collide with
neutral gas molecules such as helium or nitrogen.
The collisions break the bonds and fragment the ions
into smaller pieces.
contact closure connection The cable connection is
from the external peripheral device to the mass
spectrometer contact closure pins (Start In and
Ground). The external device sends the contact
closure (start) signal to the mass spectrometer.
conversion dynode A highly polished metal surface
that converts ions from the mass analyzer into
secondary particles, which enter the electron
multiplier.
D
divert/inject valve A valve on the mass spectrometer
that can be plumbed as a divert valve or as a loop
injector.
fragment ion A charged dissociation product of an
ionic fragmentation. Such an ion can dissociate
further to form other charged molecular or atomic
species of successively lower formula weights.
full-scan type Provides a full mass spectrum within a
defined mass range.
H
heated-electrospray (H-ESI) Converts ions in
solution into ions in the gas phase by using
electrospray (ESI) in combination with heated
auxiliary gas.
heated-electrospray ionization (H-ESI) See heatedelectrospray (H-ESI).
high performance liquid chromatography (HPLC)
Liquid chromatography where the liquid is driven
through the column at high pressure. Also known as
high pressure liquid chromatography.
I
E
electron multiplier A device used for current
amplification through the secondary emission of
electrons. Electron multipliers can have a discrete
dynode or a continuous dynode.
electrospray (ESI) A type of atmospheric pressure
ionization that is currently the softest ionization
technique available to transform ions in solution into
ions in the gas phase.
electrospray ionization (ESI) See electrospray (ESI).
image current detection The detection of ion motion
by the charge (current) induced on one or more
capacitive plates (outer electrodes).
ion detection system A high sensitivity, off-axis
system for detecting ions. It produces a high signalto-noise ratio (S/N) and allows for switching of the
voltage polarity between positive ion and negative
ion modes of operation. The ion detection system
includes two ±12 kVdc conversion dynodes and a
discrete dynode electron multiplier.
F
ion isolation A step in the quadrupole Q1 mass
analysis where the mass analyzer ejects all ions except
for the ions of interest.
flow rate, syringe pump status The syringe pump
injection flow rate in milliliters per minute (mL/min)
or microliters per minute (μL/min) for the current
sample, as defined in the current experiment method.
ion isolation waveform voltage A waveform applied
to the linear ion trap that ejects all ions except the
SIM ion or precursor ion.
forepump The pump that evacuates the foreline. A
rotary-vane pump is a type of forepump. It might
also be referred to as a backing, mechanical, rotaryvane, roughing, or vacuum pump.
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ion optics Focuses and transmits ions from the API
source to the mass analyzer.
Thermo Scientific
Glossary: ion polarity mode
ion polarity mode The mass spectrometer can operate
in either of two ion polarity modes: positive or
negative.
ion sweep cone A removable cone-shaped metal cover
that fits on top of the API ion transfer tube and acts
as a physical barrier to protect the entrance of the
tube.
L
LC pump A high pressure solvent pump in the LC
that provides the pressure on the input side of a
column to drive the eluent and sample through the
column.
lens A metal disk with a circular hole in the center that
allows the ion beam to pass.
M
mass analysis A process that produces a mixture of
ionic species that is then separated according to the
mass-to-charge ratios (m/z) of the ions to produce a
mass spectrum.
mass analyzer A device that determines the mass-tocharge ratios (m/z) of ions by one of a variety of
techniques.
mass analyzer dc offset voltage A dc voltage that is
applied to the mass analyzer electrodes to help draw
ions in from the ion optics. This voltage defines the
translational kinetic energy of the ions as they enter
the mass analyzer. For the mass detector, the mass
analyzer dc offset voltage is –10 Vdc for positive ions
and +10 Vdc for negative ions.
mass spectrometer An instrument that ionizes sample
molecules and then separates the ions according to
their mass-to-charge ratio (m/z). The resulting mass
spectrum is a characteristic pattern for the
identification of a molecule.
mass spectrum A graphical representation (plot) of
measured ion abundance versus mass-to-charge ratio.
The mass spectrum is a characteristic pattern for the
identification of a molecule and is helpful in
determining the chemical composition of a sample.
Thermo Scientific
mass-to-charge ratio (m/z) An abbreviation used to
denote the quantity formed by dividing the mass of
an ion (in Da) by the number of charges carried by
the ion. For example, for the ion C7H72+,
m/z = 45.5.
molecular ion An ion formed by the removal (positive
ion) or addition (negative ion) of one or more
electrons to/from a molecule without fragmentation
of the molecular structure.
multipole A symmetrical, parallel array of (usually)
four, six, or eight cylindrical rods that acts as an ion
transmission device. An rf voltage and dc offset
voltage are applied to the rods to create an
electrostatic field that efficiently transmits ions along
the axis of the multipole rods.
multipole dc offset voltage A dc voltage applied to a
multipole rod assembly. The multipole dc offset
voltage helps to define the translational kinetic
energy of the ions within the assembly.
multipole rf voltage The amplitude of the rf voltage
applied to the multipoles.
N
nanoelectrospray ionization (nanoESI or NSI) A
type of electrospray (ESI) that accommodates very
low flow rates of sample and solvent at 1–20 nL/min
(for static nanoelectrospray) or 100–1000 nL/min
(for dynamic nanoelectrospray, which is also called
nanoESI nanoLC gradient separation).
nanoESI nanoLC gradient separation Employs
microscale capillary columns to separate the analytes
in complex mixtures. The sample is loaded onto a
column using an injection valve or a gas pressure
vessel. The mixture components are then eluted by a
solvent gradient and pumped through the emitter.
neutral loss mass The mass of the neutral species that
is lost by the precursor ion in a neutral loss
experiment.
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Glossary: neutral loss scan mode
neutral loss scan mode A scan mode that links
together an MS and MS/MS scan so that they are
scanned at the same rate over scan ranges of the same
width. However, the respective mass ranges are offset
by a selected mass so that the MS/MS scan is a
selected number of mass units lower than the MS
scan.
P
peak threshold The minimum number of intensity
counts per sampling interval that is required before a
signal is recorded.
peak width The distance across a peak measured at a
selected peak-height level, in minutes or mass units.
The peak-height level is usually specified as a
percentage of the maximum peak height.
peak width at half height The full width of a peak at
half its maximum height, sometimes abbreviated
FWHM.
precursor ion An electrically charged molecular
species that can dissociate to form fragments. The
fragments can be electrically charged or neutral
species. A precursor ion can be a molecular ion or an
electrically charged fragment of a molecular ion.
precursor mass The mass-to-charge ratio of a
precursor ion. The location of the center of a target
precursor-ion peak in mass-to-charge ratio (m/z)
units.
product ion An electrically charged fragment of an
isolated precursor ion.
product mass The mass-to-charge ratio of a product
ion. The location of the center of a target production
peak in mass-to-charge ratio (m/z) units.
profile data Data representing mass spectral peaks as
point-to-point plots, with each point having an
associated intensity value.
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Q
qualitative analysis Chemical analysis designed to
determine the identity of the components of a
substance.
quantitative analysis Chemical analysis designed to
determine the quantity or concentration of a specific
substance in a sample.
R
retention time (RT) The time after injection at which
a compound elutes. The total time that the
compound is retained on the chromatograph
column.
rf lens A multipole rod assembly that is operated with
only radio frequency (rf ) voltage on the rods. In this
type of device, virtually all ions have stable
trajectories and pass through the assembly.
rf voltage (linear ion trap) An ac voltage of constant
frequency and variable amplitude that is applied to
the quadrupole rods of a multipole. Because the
frequency of this ac voltage is in the radio frequency
(rf ) range, it is referred to as rf voltage.
S
sample loop A loop of calibrated volume that is used
to perform flow injection analysis.
scan Comprised of one or more microscans. Each
microscan is one mass analysis (ion injection and
storage/scan-out of ions) followed by ion detection.
After the microscans are summed, the scan data is
sent to the data system for display and/or storage.
The process of ramping the amplitude of the rf and
dc voltages on the multipole rods in the mass
analyzer to transmit ions from the lowest mass to the
highest mass of a specified scan range.
selected ion monitoring (SIM) scan type A scan type
where the mass spectrometer acquires and records ion
current following the isolation of a range of mass-tocharge ratio values.
Thermo Scientific
Glossary: selected reaction monitoring (SRM) scan type
selected reaction monitoring (SRM) scan type A
scan type with two stages of mass analysis and where
a particular reaction or set of reactions, such as the
fragmentation of an ion or the loss of a neutral
moiety, is monitored. In SRM a limited number of
product ions is monitored.
sheath gas The inner coaxial gas (nitrogen), which is
used in the API source to help nebulize the sample
solution into a fine mist as the sample solution exits
the ESI or APCI nozzle.
signal-to-noise ratio (S/N) The ratio of the signal
height (S) to the noise height (N). The signal height
is the baseline corrected peak height. The noise
height is the peak-to-peak height of the baseline
noise.
source See API source.
static nanoelectrospray A device that performs
continuous analysis of small analyte solution volumes
over an extended period of time.
sweep gas Nitrogen gas that flows out from behind
the sweep cone in the API source. Sweep gas aids in
solvent declustering and adduct reduction.
syringe pump A device that delivers a solution from a
syringe at a specified rate.
T
turbomolecular pump A vacuum pump that provides
a high vacuum for the mass spectrometer and
detector system.
V
vacuum manifold A thick-walled, aluminum
chamber, with various electrical feedthroughs and gas
inlets, which encloses the API stack, ion optics, mass
analyzers, and ion detection system.
vacuum system Components associated with lowering
the pressure within the mass spectrometer. A vacuum
system includes the vacuum manifold, pumps,
pressure gauges, and associated electronics.
Thermo Scientific
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95
I
Index
A
active beam guide, MP0 37
active collision cell (Q2) 39
air leaks
checking 61
fixing 61
API cone seal 73
API gas valves, description 26
API gases
See gases
API modes 30
API source
description 30
housing, cleaning 69
API source interface
description 31
ion transfer tube 31
reinstalling 80
removing 75
replaceable parts 89
argon gas, checking the pressure 62
autosampler, starting 54
auxiliary gas, description 26
C
calibration parameters, resetting to default values 55
Cautions
replacing fuses 84
replacing PCBs and power supplies 84
cleaning procedures
API source housing 69
exit lens 79
lens L0 79
MP00 rf lens 79
rf lens 79
syringe 63
collision cell efficiency 41
collision energy (Q2 offset voltage) 42
Thermo Scientific
collision gas 41
collision pressure vacuum gauge 27
communication connectors 9
communication LED, description 7
compliance
FCC iii
regulatory iii
cone seal, API 73
contact closure cable control, connecting with MS
application 10
contact closure interface 8
contacting us xvii
contamination, preventing 66, 71
controls and indicators 6
convection gauge, description 27
See also vacuum system, gauges
cooling fans, description 11
customer responsibility 65
D
daily tasks 59
data system, starting 53
data types 20
diagnostics 83
Caution 83
running 83
directive, WEEE v
divert/inject valve 46
documentation
accessing xiv
additional xiii
downloading xiv
dual-mode discrete dynode, description 43
E
electromagnetic compatibility iii
electron multiplier gain 43
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Index: F
electronic assemblies 6
electronics service switch
description 8
location 7
EMC compliance iii
emergency shutdown 49
exit lens
cleaning 79
description 32
reinstalling 79
removing 77
F
fans
description 11
filter, cleaning 80
FCC compliance iii
figures, list of xi
flushing the inlet components 63
forepump
control connector, MS 8
description 28
oil purging 63
functional block diagrams
LC/MS 5
vacuum system 24
fuses, replacing in MS 84
G
gases
internal schematic drawing 24
nitrogen, description 26
supply levels, checking 62
gloves, part numbers 69
H
hyperquads Q1 and Q3, description 38
I
inlet components, flushing 63
inlet gases hardware, description 25
ion detection system 43
ion gauge, description 27
ion optics
description 35
MP0 37
MP00 rf lens, cleaning 79
MP00, description 36
ion polarity modes 21
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TSQ Endura and TSQ Quantiva Hardware Manual
ion pressure vacuum gauge 27
ion sweep cone
cleaning 74
description 31
figure of 72
gas inlet location 73
removing 71
ion transfer tube
cleaning 73–74
description 31
drawing of 73
installing 74
removal tools 72
removing 70
ion transmission device, rod assembly 14
ionization technique, description 3
K
kits
Calibration 86
Dual Mechanical Pumps 88
MS Setup 87
Performance Specification 87
Single Mechanical Pump 88
TSQ Chemical 85
TSQ Source Installation 89
L
LC/MS analysis, description 3
LEDs 6
lenses
EL21, EL22, EL23, EL31, EL32, and EL33 42
L0
cleaning 79
description 36
removing 77
L4 43
TK1 and TK2 37
line power, specification 7
liquid chromatograph
solvent flow, turning off 51, 71
starting 53
loop injection 47
M
main power switch, description 8
maintenance
API source housing, cleaning 69
fan filter, cleaning 80
forepump oil, purging 63
schedule 66
Thermo Scientific
Index: N
mass analysis, discussion 41
mass analyzer
description 14, 38
rf and dc voltages 39
mass range 20
mass spectrometer
emergency shutdown 49
functional block diagram 5
functional description 23
gas inlet ports, locations 25
ion polarity modes 21
mass range 20
on/off status for components, voltages, and gas
flows 56
photos 2
power panel 7
resetting 54
scan types 13
shutting down 51
shutting down completely xvi
Standby mode 50
starting 53
turning on 51
vacuum manifold 27
vacuum system 23
metal needle insert for H-ESI spray insert 66
MP00 rf lens
cleaning 79
removing 77
MS scan types 14–15
MS/MS scan types 20
neutral loss scan type 18
product scan type 15
See scan types
N
nitrogen gas
inlets assembly, description 26
pressure 26
pressure, checking 62
rate of consumption 62
O
offset voltage, quadrupole 42
on/off status for MS components 56
O-rings
API source interface, under 76
ion transfer tube, under 73
Thermo Scientific
P
parts
See replaceable parts
PCBs 6
power
entry module 7
LED description 6
specifications 7
power supply cord xvi
power switch, location 7
pressure gauges, note about 54
pressures levels, checking 60
pressures, vacuum manifold regions 27
pump down time 54
Q
quadrupole mass analyzers
functional description 41
quadrupole offset voltage 42
R
readback values, vacuum gauges 27
regulatory compliance iii
relay switch circuit 10
replaceable parts, part numbers 85
reset button 8
rf lens
cleaning 79
description 32
reinstalling 79
removing 77
S
safety precautions xvi
safety standards iii
sample transfer line, flushing 62
sample tube, flushing 62
scan LED, description 7
scan types
discussed 13
MS scans
full scan Q1 and Q3 14
selected ion monitoring (SIM) 15
MS/MS scans
neutral loss 18
precursor 17
product 15
selected reaction monitoring (SRM) 20
summary of 14
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Index: T
sheath gas, description 26
shutdown
emergency procedure 49
mass spectrometer 51
solvent waste container, emptying 64
source pressure vacuum gauge 27
spray cone, cleaning 73
spray insert, cleaning 62
Standby mode 50
sweep cone
See ion sweep cone
sweep gas, description 26
switches, MS 7
syringe adapter assembly, drawing 46
syringe pump
default flow rate 45
description 45
syringe, cleaning 63
system checks
argon and nitrogen supplies 62
vacuum levels 60
system LED, description 7
system startup 52
ion pressure 27
source pressure 27
pressure levels, checking 60
vent valve, description 26
voltages
line power specifications 7
quadrupole offset 42
W
WEEE directive v
T
translational kinetic energy (TKE) 36
troubleshooting 83
Tune, opening 50
turbomolecular pump, description 28
U
USB ports, pin-out descriptions 11
V
vacuum LED
description 7
note about pressure 54
vacuum manifold
description 27
pressures 27
vacuum regions 27
vacuum pressure levels, checking 60
vacuum pumps
See turbomolecular pumps
vacuum system
description 23
functional block diagram 24
gauges
collision pressure 27
convection 27
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Thermo Scientific
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